I have compiled a crossreference of the Brookhaven Protein Data Bank
files which may be of use to others. If you find errors in this
listing please let me know.
/*
This file was compiled by Laura Lynn Walsh, Beckman Institute,
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801-2325
(217) 244-6764 lwalsh at nemo.life.uiuc.edu
Date begun: November, 1990
Latest revision: November, 1991
This file is an annotation of all of the Brookhaven Protein Data
Bank files with actual coordinates. (The files beginning with
pdb0 have been omitted until full coordinates are available.)
The information has been taken from the Brookhaven Protein Data
Bank and from original papers by authors listed in those files.
Responsibility for the accuracy of the information is LLW's,
who would welcome reports of errors and suggestions to extend
the usefulness of the information. This information is provided
for your use and no warranty about the correctness of the infor-
mation is made.
Support from NSF-DIR90-19063 for LLW is gratefully acknowledged.
*/
/*
Description of Entries:
The header line begins with the common name for the protein or
other molecule(s) contained in the file.I have tried to use
the most commonly accepted names, but in several cases, especially
the immunoglobulin files, this has been difficult.
The molecule name is followed by its source. This is the
source of the original sequence.In several cases a protein
is actually expressed in another organism, such as E. coli,
but this is not noted in this file.
DUP = duplicate entry. This file is also listed for
another protein or other molecule. (E.g. the Eglin C
and subtilisin complex is listed under both headers.)
The file names from the Brookhaven Protein Data Bank have been
abbreviated. Where Brookhaven names the files pdbXXXX.ent,
the files are referred to here solely by the XXXX part. Files
with a "w" appended to their names are files that I have
modified to make a "complete" protein, i.e., if the protein
is a tetramer and only two of the chains are given in the
original file, the new file would contain the tetramer and
conversely, if the original file contains two chains and
the protein is a monomer, this file contains a single chain.
These files are not publicly available at present.
The columns following the PDB file name indicate the resolution
for the x-ray data. If the file is an NMR file, "NMR" is in
this field, since resolution is not applicable for these. "CA"
indicates that the entry contains coordinate information only
for the alpha carbons. "UNK" means the amino acid sequence
is unknown.
The body of the entry indicates how many chains are in the
"complete" molecule (see below), how many chains are included
in the entry, and any other information that helps distinguish
that specific entry from another similar entry. I have also
included any information I had that could help in interpreting
the data in the entry.In particular, I have attempted to
include any possible differences between the crystallographic
data and what is thought to be the active, "solution" structure
of the molecule. I am currently working on including information
about ions and crystallization conditions, but this information
should be considered incomplete.
*/
/*
"Correct" proteins are either the complete protein as seen in
the pictures accompanying the original literature or, failing
this, a protein that "looks ok" and which can be generated by
both my program and Insight (Biosym) to look the same. Failing
both of these, a correct protein is as close as I could come to
what I think is correct. If it is not, PLEASE let me know.
The "correct" proteins were generated by one of several possible
methods:
1) If there was a matrix given in the data file itself which
produced a "correct" protein, this was used.
2) If there was no applicable matrix, or if the matrix did
not generate a correct protein, the International Table for
Crystallography matrices were used. If possible, these were
checked against the matrices and proteins produced by Insight
(Biosym). Insight (Biosym) can do symmetry operations in its
Assembly module under the Symmetry command. The program uses
a 4 X 4 matrix and is thus not the same as the program I use
to make symmetry related protein chains. I use a 3 X 4 matrix.
I prefer my program for two reasons -- the atom numbering used
in the original file is retained and the symmetry related
chains are numbered 10000 more than the original atoms. This
requires renumbering when there are several symmetry operations
performed, but it makes generating CONECT records much easier.
*/
434 Cro Protein (Phage 434)
2cro 2.35 monomer in solution - 1 chain given; dimer in crystal,
but dimerizes differently when bound to DNA; Insight
can't find space group R 32; includes water
434 Repressor Protein - N Terminal Domain (Phage 434)
1r69 2.0 monomer in solution - 1 chain given; includes water
2or1 2.5 dimer in complex with dsDNA (a2 + d2) - 4 chains given
Acid Proteinase Endothiapepsin (Endothia parasitica)
4ape 2.1 monomer; sequence numbering based on pepsin; includes water
2er0 3.0 monomer; complex with inhibitor
2er6 2.0 monomer; complex with inhibitor
2er7 1.6 monomer; complex with inhibitor
2er9 2.2 monomer; complex with inhibitor
4er1 2.0 monomer; complex with inhibitor
4er2 2.0 monomer; complex with inhibitor
5er1 2.0 monomer; complex with inhibitor
Acid Proteinase Penicillopepsin (Penicillium janthinellum)
2app 1.8 monomer
3app 1.8 monomer; supersedes 2app; includes water
Acid Proteinase Rhizopuspepsin (Rhizopus chinensis)
2apr 1.8 monomer; supersedes 1apr; includes Ca++
3apr 1.8 monomer; complex with reduced peptide inhibitor
4apr 2.5 monomer; complex with a pepstatin-like renin inhibitor
5apr 2.1 monomer; complex with a pepstatin-like renin inhibitor
6apr 2.5 monomer; complex with pepstatin
Aconitase (Sus scrofa)
5acn 2.1 monomer; inactive 3Fe-4S form
6acn 2.5 monomer; active 4Fe-4S form; includes sulfate, tricar-
ballylic acid and water
Actinidin (Actinidia chinensis)
2act 1.7 monomer; supersedes 1act; includes oxygens, ammonium,
and water
Actinoxanthin (Actinomyces globisporus, number 1131)
1acx 2.0 monomer
Adenylate Kinase (Sus scrofa)
3adk 2.1 monomer; supersedes 2adk; includes sulfates
Agarose (Rhodophycae)
1aga 3.0 sugar polymer; NOT PROTEIN
Alamethicin (Trichoderma viride)
1amt 1.5 3 chains given; contains many AIBs & 3 PHLs
Alcohol Dehydrogenase (Equus caballus)
5adh 2.9 dimer (a2) - 1 chain given; apo; complex with ADP-ribose
6adh 2.9 dimer (a2) - 2 chains given; holo; complex with NAD & DMSO
7adh 3.2 dimer (a2) - 2 chains given; isonicotinamidylated
8adh 2.4 dimer (a2) - 1 chain given; apo
8adhw dimerized acc to included matrix
Alpha-Amylase Inhibitor HOE-467A (Streptomyces tendae, 4158)
1hoe 2.0 monomer
Alpha-Lytic Protease (Lysobacter enzymogenes)
1p01 2.0 complex with substrate analogs
1p02 2.0 complex with substrate analogs
1p03 2.15 complex with substrate analogs
1p04 2.55 complex with substrate analogs
1p05 2.10 complex with substrate analogs
1p06 2.34 complex with substrate analogs
1p07 2.25 complex with substrate analogs
1p08 2.25 complex with substrate analogs
1p09 2.20 complex with substrate analogs
1p10 2.25 complex with substrate analogs
2alp 1.7 monomer; gaps in numbering
Alpha-1 Proteinase Inhibitor (Homo sapiens)
Cleavage of original monomer yields 2 or 3 chains - 3rd "chain" is
a single Cys residue.
5api 3.0 2 chains given; modified; bond cleavage results in large
structural change; superseded by 7api
6api 3.0 2 chains given; modified; bond cleavage results in large
structural change; active structure may be quite different;
superseded by 8api
7api 3.0 3 chains given; modified; structural change; tetragonal form 1;
supersedes 5api
8api 3.1 3 chains given; modified; structural change; hexagonal form;
supersedes 6api
9api 3.0 3 chains given; modified; structural change; tetragonal form 2
Apolipoprotein D (Homo sapiens)
1apd --- model; non-experimental
L-Arabinose binding protein (Escherichia coli)
1abp 2.4 monomer
Aspartate Aminotransferase (Gallus gallus)
1aat 2.8 CA complex with 2-oxo-glutaric acid
Aspartate Aminotransferase (Escherichia coli)
2aat 2.8 dimer (a2) - 1 chain given; mutant K258A; complex with
pyridoxamine phosphate;
2aatw made; checked on Iris
Aspartate Carbamoyltransferase (Escherichia coli)
2atc 3.0 dodecamer (3[a2b2]) - 2 chains given; unliganded
4atc 2.6 dodecamer (3[a2b2]) - 4 chains given; unliganded;
superseded by 6at1
7atc 2.6 dodecamer (3[a2b2]) - 4 subunits; complex with CTP;
supersedes 5atc; superseded by 5at1
8atc 2.5 dodecamer (3[a2b2]) - 4 chains given; R state;
complex with PALA
1at1 2.8 dodecamer (3[a2b2]) - 4 chains given; R state;
complex with PAM & MAL
2at1 2.8 dodecamer (3[a2b2]) - 4 chains given; R state;
complex with PAM & MAL
3at1 2.8 dodecamer (3[a2b2]) - 4 chains given; T state; complex with PAM
4at1 2.6 dodecamer (3[a2b2]) - 4 chains given; T state; complex with ATP
5at1 2.6 dodecamer (3[a2b2]) - 4 chains given; T state; complex with CTP;
supersedes 7atc
6at1 2.6 dodecamer (3[a2b2]) - 4 chains given; T state; supersedes 4atc
7at1 2.8 dodecamer (3[a2b2]) - 4 chains given; R state;
complex with PAM, MAL, & ATP
8at1 2.8 dodecamer (3[a2b2]) - 4 chains given; R state;
complex with PAM, MAL, & CTP
ATX 1A (Anemonia sulcata)
1atx NMR monomer - 8 chains given; lowest energy conformation is model 1
Azurin (Alcaligenes denitrificans)
2aza 1.8 monomer - 2 chains given; oxidized
2azaw half of coords eliminated; monomer remains; there are a lot
of contacts between the independent molecules in the crystal
Azurin (Pseudomonas aeruginosa)
1azu 2.7 monomer
Bacteriochlorophyll-A Protein (Prosthecochloris aestuarii, strain 2K)
3bcl 1.9 monomer; many UNK residues; all ASP & ASN are ASX;
all GLU & GLN are GLX
Bacteriorhodopsin (Halobacterium halobium)
1brd 3.5* monomer; resolution 3.5 in x and y directions, 10.0 in z
BDS-1 (Anemonia sulcata)
1bds NMR monomer; averaged structure
2bds NMR monomer - 42 simulated annealing structures
Bean Pod Mottle Virus - Middle Component (Bountiful bean)
1bmv 3.0 120mer + RNA (60ab + r) - 3 chains given; unusual numbering
system; Insight can't find space group P 2 21 21
Alpha Bungarotoxin (Bungarus multicinctus)
related to Cobratoxin
2abx 2.5 dimer (a2) - 2 chains given; due to crystal contacts, Phe
sticks out into solvent - near to another Phe in a neighboring
molecule
Calcium-Binding Parvalbumin B (Cyprinus carpio)
1cdp 1.6 monomer; Cadmium substituted
1cpv 1.85 monomer
2cpv 1.85 monomer
3cpv 1.85 monomer
4cpv 1.5 monomer; pI 4.25
5cpv 1.6 monomer; supersedes 1cpv, 2cpv, 3cpv; due to crystal contacts,
phe sticks out into solvent - near to another phe in a
neighboring molecule
Calcium-Binding Protein (Bos taurus)
3icb 2.3 monomer; supersedes 2icb;
Calmodulin (Bos taurus)
2cln --- trimethyl Cln complex with trifluroperazine; non-exp'l model
3cln 2.2 monomer
Carbonic Anhydrase I, Form B (Carbonate Dehydratase) (Homo sapiens)
2cab 2.0 monomer
Carbonic Anhydrase II (Homo sapiens)
1ca2 2.0 monomer
2ca2 1.9 monomer; complex with thiocyanate ion
3ca2 2.0 monomer; complex with AMS
Carboxypeptidase A (Bos taurus)
3cpa 2.0 monomer; alpha; complex with glycyl-L-tyrosine
4cpa 2.5 monomer; alpha; complex with inhibitor
5cpa 1.54 monomer; alpha
Carboxypeptidase B (Bos taurus)
1cpb 2.8 CA monomer; fraction II
D-Alanyl-D-Alanine Carboxypeptidase/Transpeptidase (Streptomyces r61)
1pte 2.8 CA seq uncertain
Capsular Polysaccharide (Escherichia coli)
1cap 3.0 from mutant; NOT PROTEIN
Cardiotoxin V4 (Naja mossambica mossambica)
1cdt 2.5 2 chains given
Catabolite Gene Activator Protein (Escherichia coli)
2gap --- complex; model
3gap 2.5 dimer (a2) - 2 chains given - have diff configurations;
complex with cyclic AMP
Catalase (Penicillium vitale)
4cat 3.0 all residues listed as UNK
Catalase (Bos taurus)
7cat 2.5 tetramer (a4) - 1 chain given
8cat 2.5 tetramer (a4) - 2 chains given
8catw tetramerized acc. to instructions; doesn't correspond
to any replicate generated by Insight and matrix does
not correspond to one in the International Tables;
literature does not show picture of complete molecule
CD4 (Homo sapiens)
1cd4 2.3 monomer; N-terminal fragment
Cellobiohydrolase I (C terminal domain) (Trichoderma reesei)
1cbh NMR monomer; averaged structure
2cbh NMR 41 structures; simulated annealing
Cellobiohydrolase II Core Protein (Trichoderma reesei)
3cbh 2.0 CA dimer (a2) - 1 chain given
Che-Y (Salmonella typhimurium)
2chy 2.7 CA monomer; mutant (S56C)
Chloramphenicol Acetyltransferase - Type III (Escherichia coli)
1cla 2.34 trimer (a3) - 1 chain given; mutant (S148A)
2cla 2.35 trimer (a3) - 1 chain given; mutant (D199N)
3cla 1.75 trimer (a3) - 1 chain given; complex with chloramphenicol
3claw trimerized acc. to included matrices; checked on Iris
Chondroitin-4-Sulfate (Bos taurus)
1c4s 3.0 NOT PROTEIN
2c4s complex; NOT PROTEIN
Chymosin B (Bos taurus)
1cms 2.3 monomer; crystal packing as done by Insight doesn't look
like crystal packing in literature -- I: molecules are
back to back; L: molecules are front to back
Chymotrypsin Alpha (Bos taurus)
same seq as gamma
1cho 1.8 monomer + inhibitor (a + b) - 2 chains given; complex with
ovomucoid 3rd domain (inhibitor)
2cha 2.0 monomer; tosylated; EXC codes for excised residues
4cha 1.68 monomer - 2 chains given; EXC codes for excised residues
5cha 1.67 "dimeric structural unit" - 2 chains given; same as for 4cha
6cha 1.8 "dimeric structural unit" - 2 chains given; complex with PEBA
Chymotrypsin Gamma (Bos taurus)
same seq as alpha
2gch 1.9 monomer
3gch 1.9 monomer; with cinnamate
4gch 1.9 monomer; with cinnamate
5gch 2.7 monomer; photolysis product of inhibited molecule
6gch 2.1 monomer; with inhibitor APF
7gch 1.8 monomer; with inhibitor LF
Chymotrypsin Inhibitor 2 (Hordeum vulgare, hiproly strain)
2ci2 2.0 monomer
Chymotrypsinogen A (Bos taurus)
1chg 2.5 monomer; alpha; zymogen
2cga 1.8 monomer - 2 chains given; alpha; zymogen; extensive
contacts between monomers
2cgaw half of coords eliminated; monomer remains
Citrate Synthase (Gallus gallus)
3cts 1.7 UNKdimer (a2) - 1 chain given; complex with CO-A & citrate;
residues all UNK;
5cts 1.9 dimer (a2) - 1 chain given; complex with oxaloacetate &
CO-A; seq inferred from Sus scrofa (4cts); same form
as 2cts, presumably monoclinic, closed
5ctsw made; checked on Iris; has protruding N-terminus in
contact with neighboring dimer
6cts 2.5 dimer (a2) - 1 chain given; complex with citrylthioether
& CO-A; seq as 5cts
Citrate Synthase (Sus scrofa)
1cts 2.7 dimer (a2) - 1 chain given; complex with citrate
2cts 2.0 dimer (a2) - 1 chain given; complex with CO-A & citrate;
monoclinic form (closed)
2ctsw dimer made; checked on Iris; has protruding N-terminus in
contact with neighboring dimer
4cts 2.9 dimer (a2) - 2 chains given; complex with oxaloacetate & CO-A;
tetragonal form (open)
Alpha Cobratoxin (Naja naja siamensis)
related to Bungarotoxin
1ctx 2.8 monomer
Concanavalin A (Canavalia ensiformis)
1cn1 3.2 dimer (a2) - 2 chains given; demetallized
2cna 2.0 dimer or tetramer (a2 or a4) - 1 chain given
2cnaw made; checked
3cna 2.4 dimer or tetramer (a2 or a4) - 1 chain given
Crambin (Crambe abyssinica)
1crn 1.5 monomer
Cro Repressor Protein (Phage lambda)
1cro 2.2 CA 4 chains in data set (O,A,B,C); O-B thought to be
functional unit
Crystallin Gamma II (Bos taurus)
1gcr 1.6 monomer
Crystallin Gamma IV (Bos taurus)
2gcr 2.3 monomer; but packs tightly in vivo under some conditions
Cucumber Basic Protein (Cucumis sativus)
1cbp 2.5 CA
C-AMP Dependent Protein Kinase (Bos primigenius Taurus)
1apk --- model of Type I - Domain A
2apk --- model of Type I - Domain A
1bpk --- model of Type I - Domain B
2bpk --- model of Type I - Domain B
Cytochrome B5 (Bos taurus)
membrane binding tail removed
2b5c 2.0 monomer; oxidized
3b5c 1.5 monomer; oxidized; supersedes 2b5c
Cytochrome B562 (Escherichia coli)
156b 2.5 monomer; oxidized
256b 1.4 monomer - 2 chains given; oxidized; supersedes 156b
256bw made; checked
Cytochrome C (Katsuwonis pelamis, linnaeus or Thunnus alalunga)
seq same in T. alalunga & K. pelamis; Thunnus acetylated at N terminus
1cyc 2.3 monomer; ferro; Katsuwonis
3cyt 1.8 dimer (a2) - 2 chains given; oxidized; Thunnus
5cyt 1.5 monomer; reduced; Thunnus
Cytochrome C (Oryza sativa l.)
1ccr 1.5 monomer
Cytochrome C - Isozyme 1 (Saccharomyces cerevisiae)
1ycc 1.23 monomer?; reduced; one residue is actually trimethyllysine
Cytochrome C Peroxidase (Saccharomyces cerevisiae)
2cyp 1.7 monomer
1ccp 2.2 monomer; native + two N-terminal aa's from expression in E.coli;
sequence differs from 2cyp at 2 aa's -- strain-related
2ccp 2.2 monomer; D235N mutant of 1ccp
3ccp 2.2 monomer; W191F mutant of 1ccp
4ccp 2.2 monomer; W51F mutant of 1ccp
Cytochrome C Prime (Rhodospirillum molischianum)
2ccy 1.67 dimer (a2) - 2 chains given
Cytochrome C2 (Rhodospirillum rubrum)
2c2c 2.0 monomer; oxidized
3c2c 1.68 monomer; reduced
Cytochrome C3 (Desulfovibrio desulfuricans Norway)
1cy3 2.5 monomer
Cytochrome C3 (Desulfovibrio vulgaris miyazaki iam 12604)
2cdv 1.8 monomer
Cytochrome C5 (Azotobacter vinelandii)
1cc5 2.5 monomer
Cytochrome C550 (Paracoccus denitrificans)
155c 2.5 monomer; some UNK residues at C terminus
Cytochrome C551 (Pseudomonas aeruginosa)
351c 1.6 monomer; oxidized
451c 1.6 monomer; reduced
Cytochrome P450CAM (Camphor Monooxygenase) (Pseudomonas putida)
2cpp 1.63 monomer; with bound camphor
3cpp 1.9 monomer; with reduced camphor & CO
4cpp 2.11 monomer; with adamantane
5cpp 2.08 monomer; with adamantane
6cpp 1.9 monomer; with camphane
7cpp 2.0 monomer; with norcamphor
8cpp 2.1 monomer; with thiocamphor
Cytotoxic T-Lymphocyte Proteinase I (Mus musculus)
2cp1 --- non-experimental model
Deoxyribonucleic Acid (DNA)
1ana 2.1 tetramer
1bd1
1bna
1d10
1d11
1d12
1d13
1d14
1d15
1d16
1d17
1d18
1d19
1d20
1d21
1d22
1dcg
1dn4
1dn5
1dn6
1dn7
1dn8
1dn9
1dne
1dnf
1dnh
1dnm
1dnn
1dns
1zna
2ana
2bna
2dcg
2dnd 2.2 complex with distamycin
2zna
3ana
3bna
3dnb
3zna
4bna
4dnb
5ana
5bna
Dihydrofolate reductase (Escherichia coli)
4dfr 1.7 monomer - 2 independent chains given; chain B
preferred for structural comparisons; resistant
strain; complex with methotrexate
4dfrw half of coords eliminated; monomer remains
5dfr 2.3 monomer; apo; resistant strain
6dfr 2.4 monomer; complex with NADP+; resistant strain
7dfr 2.5 monomer; complex with folate & NADP+; resistant strain
Dihydrofolate reductase (Gallus gallus)
8dfr 1.7 monomer
Dihydrofolate reductase (Homo sapiens)
1dhf 2.3 monomer - 2 chains given; complex with folate; chain B
preferred
1dhfw chain B; half of coords eliminated; monomer remains
2dhf 2.3 monomer; complex with 5-deazafolate
Dihydrofolate reductase (Lactobacillus casei)
3dfr 1.7 monomer; complex with NADPH & methotrexate
DNA Polymerase I Klenow Fragment (Escherichia coli)
1dpi 2.8 CA
Eco R1 Endonuclease (Escherichia coli)
1r1e 2.7 CA dimer (a2) - 1 chain given; complex with DNA
Eglin C (Hirudo medicinalis)
DUP1cse 1.2 monomer; complex with subtilisin; duplicate listing
DUP1tec 2.2 monomer; complex with thermitase; duplicate listing
Elastase, Human Neutrophil (Homo sapiens)
1hne 1.84 monomer; complex with inhibitor - Methoxysuccinyl-Ala-
Ala-Pro-Ala-Chloromethyl ketone
Elastase (Sus Scrofa)
1est 2.5 monomer; tosyl
2est 2.5 monomer; complex with trifluoro-L-lysyl-L-alanyl-
P-trifluoromethyl-phenylanilide
3est 1.65 monomer; native
Elongation Factor TU (Escherichia coli B)
1efm 2.7 CA trypsin modified; excised residues labeled EXC
1etu 2.9 monomer; domain I (part of molecule not included
in data set); complex with guanosine diphosphate;
excised residues labeled EXC
Enolase (2-Phospho-D-Glycerate Hydrolase) (Saccharomyces cerevisiae)
2enl 2.25CA dimer (a2) - 1 chain given
Erabutoxin (Laticauda semifasciata)
1nxb 1.38 monomer; "B"; differs from 5ebx by one residue; inverted pair -
res 6 and 7 differ from 5ebx and 3ebx
3ebx 1.4 monomer; B; differs from 5ebx by one residue
5ebx 2.0 monomer; A; differs from 3ebx by one residue
Ferredoxin (Azotobacter vinelandii)
4fd1 1.9 monomer; supersedes 3fd1
1fd2 1.9 monomer; mutant C20A
2fd2 1.9 monomer; mutant C24A
Ferredoxin (Bacillus thermoproteolyticus)
1fxb 2.0 monomer
2fxb 2.3 monomer; supersedes 1fxb
Ferredoxin (Peptococcus aerogenes)
1fdx 2.0 monomer
Ferredoxin (Spirulina platensis)
3fxc 2.5 monomer
Ferredoxin NADP+ Oxidoreductase (Spinacia oleracea)
1fnr 2.2 monomer?
2fnr 3.0 monomer?; complex with 2'phospho 5' AMP
FK506 Binding Protein (Homo sapiens)
1fkf 1.7 monomer; complex with FK506 immunosuppressant
Flavocytochrome B2 (Saccharomyces cerevisiae)
1fcb 2.4 dimer? - 2 chains given; looks better as tetramer
Flavodoxin (Clostridium MP)
3fxn 1.9 monomer; oxidized form
4fxn 1.8 monomer; semiquinone form
Flavodoxin (Desulfovibrio vulgaris)
1fx1 2.0 monomer
D-Galactose/D-Glucose Binding Protein (Escherichia coli B/R)
1gbp 3.0 CA all residues UNK
2gbp 1.9 monomer complex with beta-D-glucose and Ca++
3gbp 2.4 monomer complex with glucose and Ca++; supersedes 1gbp
Gene 5 DNA Binding Protein (Filamentous bacteriophage FD M13)
2gn5 2.3 dimer (a2) - 1 chain given
2gn5w made; checked with Insight; structures same as lit
Glucagon (Sus scrofa)
related to insulin and avian pancreatic peptide
1gcn 3.0 trimer in crystal (a3) - 1 chain given; monomer in solution;
high temperature factors; presumed to be in crystaline
configuration on the receptor
1gcnw made; checked
D-Glucose 6-Phosphate Isomerase (Sus scrofa)
1pgi 3.5 CA dimer (a2) - 1 chain given; all residues UNK
Glutamine Synthase (Salmonella typhimurium)
2gls 3.5 dodecamer (a12) - 12 chains given; includes Mn++ and water
Glutathione Peroxidase (Bos taurus)
1gp1 2.0 tetramer (a4) - 2 chains given
1gp1 matrix as given in Intl Tables doesn't work -- subunits too
far apart; Insight's matrix doesn't work either -- there is
some overlap in the top two subunits and the bottom two are
too far apart -- the molecule is not compact as in the lit;
modified matrices don't seem to work either.
Glutathione Reductase (Homo sapiens)
3grs 1.54 dimer (a2) - 1 chain given; oxidized; supersedes 2grs;
3grsw 3grs.mtx; made; checked on Iris; Insight can't find
space group B 2
D-Glyceraldehyde-3-Phosphate Dehydrogenase (Bacillus Stearothermophilus)
1gd1 1.8 tetramer (a4) - 4 chains given; holo
2gd1 2.5 tetramer (a4) - 4 chains given; apo
D-Glyceraldehyde-3-Phosphate Dehydrogenase (Homarus americanus)
1gpd 2.9 tetramer (a4) - 2 chains given; complex with NAD & phosphates
1gpdw made
4gpd 2.8 tetramer (a4) - 4 chains given; apo; supersedes 2gpd
D-Glyceraldehyde-3-Phosphate Dehydrogenase (Homo sapiens)
3gpd 3.5 tetramer (a4) - 2 chains given; complex with NAD & phosphates;
3gpdw made; checked
Glycolate Oxidase (Spinacia oleracea)
1gox 2.0 octamer (a8) or tetramer (a4) (equil.) - 1 chain given
1goxw made; checked
Gramicidin A (Bacillus brevis)
1gma 0.86 dimer (a2) - 2 chains given; several amino acids are in D config
Hannuka Factor (Homo sapiens)
1hf1 --- model
Heat Shock Cognate Protein (Bos taurus)
1hsc 2.2 CA N-terminal fragment
Hemagglutinin (Influenza virus, 1968 X.31 strain)
bromelain digested (missing hydrophobic anchor)
1hmg 3.0 trimer of dimers (3[ab]) - 6 chains given; G146D mutant
2hmg 3.0 trimer of dimers (3[ab]) - 6 chains given; G146D mutant
3hmg 2.9 trimer of dimers (3[ab]) - 6 chains given; L226Q mutant
4hmg 3.0 trimer of dimers (3[ab]) - 6 chains given; L226Q mutant;
complex with sialic acid
5hmg 3.2 trimer of dimers (3[ab]) - 6 chains given; D112G (HA2) mutant;
complex with sialic acid
Hemerythrin (Siphonosoma species)
1hr3 5.5 CA trimer (a3?) - 3 chains given; all residues UNK
Hemerythrin (Themiste dyscritum)
1hmq 2.0 octamer (a8) - 4 chains given; two chains each from two
different octamers; met
1hmqw made; checked with Insight -- seems to be the same
as the one it makes, but has big holes; checked both ways;
re-ordered literature
1hmz 2.0 octamer (a8) - 4 chains given; azidomet
Hemerythrin B (Phascolopsis gouldii)
1hrb 5.5 CA monomer
Hemoglobin (Equus caballus)
2dhb 2.8 tetramer (a2b2) - 2 chains given; deoxy; supersedes 1dhb
2dhbw made; checked; looks ok on Iris, but Insight can't make
similar molecule
2mhb 2.0 tetramer (a2b2) - 2 chains given; aquo met
Hemoglobin (Homo sapiens)
1coh 2.9 tetramer (a2b2) - 4 chains given; alpha-ferrous-carbonmonoxy;
beta-cobaltous-deoxy; T state
1hco 2.7 tetramer (a2b2) - 2 chains given; carbonmonoxy
2hco 2.7 tetramer (a2b2) - 2 chains given; carbonmonoxy; energy minimized
2hhb 1.74 tetramer (a2b2) - 4 chains given; deoxy; "best estimate of
coordinates"
3hhb 1.74 tetramer (a2b2) - 2 chains given; deoxy; "symmetry averaged"
4hhb 1.74 tetramer (a2b2) - 4 chains given; deoxy; "unrestrained
refinement"
1hho 2.1 tetramer (a2b2) - 2 chains given; A; oxy
Hemoglobin F (Fetal) (Homo sapiens)
39/146 residues of subunit G are different from subunit B of H. sapiens
adult; other subunit is the same
1fdh 2.5 tetramer (a2b2) - 2 chains given; deoxy
1fdhw made; checked
Hemoglobin S (Sickle Cell) (Homo sapiens)
1hbs 3.0 tetramer (a2b2) - 8 chains given; deoxy; differs from
Hemoglobin A by one residue; would be useful to include
region around point mutation in predictions
1hbsw half of records eliminated; only need 4 subunits, not 8
Hemoglobin S (Sickle Cell) (Odocoileus virginianus)
1hds 1.98 tetramer (a2b2) - 4 chains given
Hemoglobin (Scapharca inaequivalvis)
1sdh 2.4 dimer - 2 chains given; carbonmonoxy
2sdh 2.4 dimer - 2 chains given; deoxy
Hemoglobin III (Erythrocruorin) (Chironomous Thummi Thummi)
1eca 1.4 monomer; aquo met
1ecd 1.4 monomer; deoxy
1ecn 1.4 monomer; cyano met
1eco 1.4 monomer; carbon monoxy
Hemoglobin V (Petromyzon marinus)
2lhb 2.0 monomer or dimer - 1 chain given; cyano, met; hydrogen atoms
added by computer
Hexokinase A (Saccharomyces cerevisiae)
1hkg 3.5 monomer; complex with glucose; many UNK residues
Hexokinase B (Saccharomyces cerevisiae)
2yhx 2.1 probably multimer - 1 chain given; complex with
orthotoluoylglucosamine; many residues UNK
High Potential Iron Protein (HIPIP) (Chromatium vinosum, strain D)
1hip 2.0 monomer
Hirudin (Hirudo medicinalis)
2hir NMR monomer; wt; multiple solutions
4hir NMR monomer; K47E mutant; multiple solutions
5hir NMR monomer; energy-minimized average structure
6hir NMR monomer; K47E mutant; energy-minimized average structure
HIV-1 Protease (HIV I)
1hvp --- model; complex with substrate; non-experimental
2hvp 3.0 CA dimer (a2) - 1 chain given
3hvp 2.8 dimer (a2) - 1 chain given; 2 Cys residues replaced by ABA
3hvpw made; looks ok
4hvp 2.3 dimer (a2) - 2 chains given; complex with inhibitor; 2 Cys
residues replaced by ABA
Human Class I Histocompatibility Antigen A2 (Homo sapiens)
1hla 3.5 CA dimer (ab) - 2 chains given
Human Class I Histocompatibility Antigen A2.1 (Homo sapiens)
3hla 2.6 dimer (ab) - 2 chains given
Human Class I Histocompatibility Antigen AW 68.1 (Homo sapiens)
membrane anchor cleaved off with papain
2hla 2.6 dimer (ab) - 2 chains given
Hyaluronic Acid (synthetic & Homo sapiens)
1hya 3.0 NOT PROTEIN
2hya 3.0 NOT PROTEIN
3hya 3.0 NOT PROTEIN
4hya 3.0 NOT PROTEIN
P-Hydroxybenzoate Hydroxylase (Pseudomonas fluorescens)
1phh 2.3 dimer (a2) - 1 chain given; complex with FAD & DHB
1phhw made; no picture of dimer in lit, but same as one of
molecules made by Insight
2phh 2.7 dimer (a2) - 1 chain given; complex with PHBH & ADPR
Immunoglobulin IgA Fab Fragment Hy/Hel-10 (Mus musculus)
1hfm --- non-experimental
2hfm --- non-experimental
Immumoglobulin IgA FV Fragment Anti-Alpha1->6 Dextran 19.1.2 (Mus musculus)
1fvb --- non-experimental
2fvb --- non-experimental; energy minimized model
Immunoglobulin IgA FV Fragment Anti-Alpha 1->6 Dextran W3129 (Mus musculus)
1fvw --- non-experimental
2fvw --- non-experimental; energy minimized model
Immunoglobulin IgA(Kappa) Fab Fragment McPC603 (Mus musculus)
1mcp 2.7 H & L chains; Insight makes a trimer of dimers, which looks
like the basic crystallographic unit; re-ordered literature
2mcp 3.1 H & L chains; complex with phosphocholine
Immunoglobulin IgA(Kappa) Fab Fragment J539 (Mus musculus)
1fbj 2.6 H & L chains
2fbj 1.95 H & L chains; supersedes 1fbj
Immunoglobulin IgG1 Fab Fragment (Homo sapiens)
2fb4 1.9 H & L chains; H chain is truncated from 2ig2; some very
close crystal contacts
2ig2 3.0 H & L chains; some of sequence & conformation is taken from 1fc1
Immunoglobulin IgG1(Kappa) Fab Fragment Hy/Hel-10 (Mus musculus & Gallus gallus)
3hfm 3.0 three chains (abx) - 2 Fab & lysozyme; similar to 2hfl,
not identical
Immunoglobulin IgG1 Fab Fragment Hy/Hel-5 (Mus musculus)
2hfl 2.54 three chains (abx) - 2 Fab & lysozyme
Immunoglobulin IgG2a(Kappa) Fab Fragment (Mus musculus)
4fab 2.7 H & L chains; complex with fluorescein (antigen)
Immunoglobulin IgG2b(Kappa) Fab R19.9 (Mus musculus)
1f19 2.8 H & L chains; similar to 3hfm
Immunoglobulin IgG(Lambda) Fab New (Homo sapiens)
3fab 2.0 H & L chains; similar to 3hfm
Immunoglobulin Fab Heterologous Light Chain Dimer (Homo sapiens)
1mcw 3.5 dimer (ab) - 2 chains given; hybrid of Weir (H analog) &
MCG (L analog); chimera
Immunoglobulin Fab Bence/Jones Protein (Homo sapiens)
2rhe 1.6 dimer (a2) - 1 chain given; lambda; variable domain
2rhew made; checked
Immunoglobulin Lambda Light Chain Dimer (Homo sapiens)
1mcg 2.3 CA dimer (a2) - 2 chains given
2mcg 2.0 dimer (a2) - 2 chains given; trigonal form (deionized water);
supersedes 1mcg
3mcg 2.0 dimer (a2) - 2 chains given; orthorhombic form (ammonium
sulfate - high salt)
Immunoglobulin IgG(Kappa) Fab Bence/Jones REI (Homo sapiens)
1rei 2.0 dimer (a2) - 2 chains given; variable portion of protein
Immunoglobulin IgG1 Fc Fragment (Homo sapiens)
1fc1 2.9 dimer (a2) - 2 chains given (a2)
1fc2 2.8 dimer (a2) - 2 chains given (a + s); half of Ig given;
complex with Fragment B of Protein A
1fc2w dimerized acc to included matrix; checked; missing piece
is due to assymetry of protein fragment; original lit checked;
protein fragment at elbow in chains
Immunoglobulin IgG1 pFc' Fragment (Cavia porcellus)
1pfc 3.125 dimer (a2) - 1 chain given
1pfcw made; checked
Immunoglobulin IgE Fc' Fragment (Homo sapiens)
1ige --- model; should NOT be used
Insulin (Bos taurus)
Insulin is produced & stored as a hexamer of dimers, but it is
active as a dimer. Subunit B is the same as S. scrofa.
2ins 2.5 dodecamer (6ab) - 4 chains given; Des-Phe B1
Insulin (Sus scrofa)
Insulin is produced & stored as a hexamer of dimers, but it is
active as a dimer. Subunit B is the same as B. taurus.
1ins 1.5 dodecamer (6ab) - 4 chains given
3ins 1.5 dodecamer - 4 chains given; joint x-ray & neutron scattering;
2-Zn; has hydrogens
4ins 1.5 dodecamer - 4 chains given; supersedes 1ins
Insulin-like Growth Factor (Somatomedin) (Homo sapiens)
1gf1 --- I; non-experimental; should NOT be used
1gf2 --- II; non-experimental; should NOT be used
Interleukin-1 Beta (Homo sapiens)
different structures done by different groups
1i1b 2.0 monomer
2i1b 2.0 monomer
4i1b 2.0 monomer
Interleukin-8 Beta (Homo sapiens)
1il8 NMR dimer; energy minimized average structure
2il8 NMR dimer; 41 simulated annealing structures
Iota Carrageenan (Rhodophycae)
1car 3.0 polysaccharide; NOT PROTEIN
Isocitrate Dehydrogenase (Escherichia coli)
3icd 2.5 dimer - 1 chain given
3icdw made; checked
4icd 2.5 dimer - 1 chain given; phosphorylated
Kallikrein A (Sus scrofa)
related to tonin
2kai 2.5 complex with BPTI; chain cleaved - separate identifiers
2pka 2.05 chain cleaved - separate identifiers; 4 chains given;
2 chains should be removed before processing
2pkaw half of coords eliminated; monomer remains; checked
Keratan Sulfate (Bos taurus)
1kes 3.0 polysaccharide; NOT PROTEIN
2-Keto-3-Deoxy-6-Phosphogluconate Aldolase (Pseudomona putida)
1kga 3.5 CA trimer - 1 chain given; all residues UNK
L7/L12 50S Ribosomal Protein - C Terminal Domain (Escherichia coli, MRE 600)
1ctf 1.7 "monomer" - whole protein is a dimer, but N terminus
is thought to be required; fragment of protein
Alpha Lactalbumin (Papio cynocephalus)
1alc 1.7 monomer; sequence deduced from x-ray
Beta Lactamase (Bacillus lichenformis 749/C)
2blm 2.0 CA monomer; 2 chains given
Beta Lactamase (Staphylococcus aureus pc1)
1blm 2.5 CA
3blm 2.0 monomer?; supersedes 1blm; check lit
***********************************************************
All lactate dehydrogenases are probably tetramers, but they
seem to crystallize in unusual space groups, or else they
don't follow the crystallographic symmetry.I can't get
Insight to make a molecule that seems reasonable to me.
***********************************************************
L-Lactate Dehydrogenase (Bacillus stearothermophilus)
1ldb 2.8 tetramer (a4) - 1 chain given; apo
1ldbw made from matrices given; checked; no picture in lit
of tetramer
2ldb 3.0 tetramer (a4) - 1 chain given; complex with NAD & F1,6P
L-Lactate Dehydrogenase (Lactobacillus casei)
1llc 3.0 tetramer (a4) - 1 chain given; complex with CO2 & F1,6P
1llcw made from matrices given; checked; no picture from
original lit - difficulty getting literature cited
Lactate Dehydrogenase (Mus musculus)
2ldx 2.96 tetramer (a4) - 1 chain given; isoenzyme C4; apo; supersedes 1ldx
2ldxw made; looks ok on screen, but doesn't look like lit
Lactate Dehydrogenase (Squallus acanthias)
3ldh 3.0 tetramer (a4) - 1 chain given; M4; complex with NAD & pyruvate
6ldh 2.0 tetramer (a4) - 1 chain given; M4; apo
6ldhw made; looks different from 1llc; I checked this by changing
the non-standard space group F 4 2 2 to I 4 2 2, which uses
the right-handed coordinate system. Four of the replicates
used by Insight to create the tetramer are the same as those
mentioned in the MTRIX records.
8ldh 2.8 tetramer (a4) - 1 chain given; M4; apo; complex with citrate
1ldm 2.1 tetramer (a4) - 1 chain given; M4; complex with NAD & oxamate
Lactate Dehydrogenase (Sus scrofa)
5ldh 2.7 tetramer (a4) - 1 chain given; H4; complex with NAD & S-Lac
Lambda Repressor (Phage lambda)
1lrd 2.5 dimer (a2) - 2 chains given + dsDNA; repressor-operator complex
1lrp 3.2 CA dimer (a2) - 1 chain given; N-terminal domain
Lectin (Pisum sativum)
2ltn 1.7 tetramer (a2b2) - 4 chains given
Leghemoglobin (Lupinus luteus l)
For these entries, the 1s & 2s of a pair were refined in diff. manners.
1lh1 2.0 monomer; acetate, met
2lh1 2.0 monomer; acetate, met
1lh2 2.0 monomer; aquo, met
2lh2 2.0 monomer; aquo, met
1lh3 2.0 monomer; cyano, met
2lh3 2.0 monomer; cyano, met
1lh4 2.0 monomer; deoxy
2lh4 2.0 monomer; deoxy
1lh5 2.0 monomer; fluoro, met
2lh5 2.0 monomer; fluoro, met
1lh6 2.0 monomer; nicotinate, met
2lh6 2.0 monomer; nicotinate, met
1lh7 2.0 monomer; nitrosobenzene
2lh7 2.0 monomer; nitrosobenzene
Leucine Binding Protein (Escherichia coli, strain K12)
2lbp 2.4 monomer; similar to 2liv
Leucine/Isoleucine/Valine Binding Protein (Escherichia coli)
2liv 2.4 monomer; similar to 2lbp
Lysozyme (Gallus Gallus)
1lym 2.5 monomer - 2 chains given
2lym 2.0 monomer; 1 atm; 1.4 M NaCl
3lym 2.0 monomer; 1000 atm; 1.4 M NaCl
1lyz 2.0 monomer; unrefined coordinates
2lyz 2.0 monomer; after refinement 1
3lyz 2.0 monomer; different refinement
4lyz 2.0 monomer; different refinement
5lyz 2.0 monomer; different refinement
6lyz 2.0 monomer; different refinement
7lyz 2.5 monomer; triclinic
8lyz 2.5 monomer; iodine inactivated
9lyz 2.5 substrate only
1lzh 6.0 CA monoclinic
2lzh 6.0 CA orthorhombic
1lzt 1.97 monomer; diff refinement from 2lzt
2lzt 1.97 monomer; diff refinement from 1lzt
Lysozyme (Homo sapiens)
1lz1 1.5 monomer
Lysozyme (Meleagris gallopavo)
1lz2 2.8 CA similar to Gallus, but not identical
2lz2 2.2 monomer; difficulty obtaining original literature
Lysozyme (Phage T4 in Escherichia coli)
1lyd 2.0 monomer; synthetic coding
2lzm 1.7 monomer; supersedes 1lzm
3lzm 1.7 monomer; same as 2lzm, but better refinement
use as basis for comparison of 1lxx mutants
1l01 - 1l35 mutants of T4 lysozyme
Cytoplasmic Malate Dehydrogenase (Sus scrofa)
4mdh 2.5 dimer (a2) - 2 chains given; supersedes 2mdh
Melittin (Apis mellifera)
1mlt 2.0 tetramer (a4) - 2 chains given
2mlt 2.0 tetramer (a4) - 2 chains given; supersedes 1mlt
2mltw made; Insight (not Intl Tables) matrix; checked; looks ok
Mengo Encephalomyocarditis Virus Coat Protein (Mengo virus)
2mev 3.0 240mer - 4 chains given; supersedes 1mev
CD-7 Metallothionein-2 (Homo sapiens)
Alpha: one residue differs from Oryctolagus; 2 from Rattus
Beta: several differences
1mhu NMR alpha domain; 31 residues long
2mhu NMR beta domain; 30 residues long
CD-7 Metallothionein-2 (Oryctolagus cuniculus)
Alpha: one residue differs from Homo sapiens; 2 from Rattus
Beta: several differences
1mrb NMR alpha domain; 31 residues long
2mrb NMR beta domain; 30 residues long
CD-7 Metallothionein-2 (Rattus rattus)
Alpha: two residues differ each from Homo sapiens and from Oryctolagus.
Beta: several differences
1mrt NMR alpha domain; 31 residues long
2mrt NMR beta domain; 30 residues long
Monellin (Dioscoreophyllum cumminsii Diels)
1mon 2.75 CA heterodimer - 8 chains given
Muconolactone Isomerase (Pseudomonas putida)
1mli 3.3 CA decamer - 1 chain given
Murein Lipoproten (Escherichia coli)
mmlp --- non-experimental
Myoglobin (Aplysia limacina)
1mba 1.6 monomer; met
2mba 2.0 monomer; azide
3mba 2.0 monomer; fluoride
4mba 2.0 monomer; imidazole
Myoglobin (Phoca vitulina)
1mbs 2.5 monomer; similar to Physeter; Insight can't match space
group A 2
Myoglobin (Physeter catodon)
1mb5 1.8 monomer; carbonmonoxy; neutron study; has hydrogens
1mbc 1.5 monomer; FeII; carbonmonoxy; 260K
1mbd 1.4 monomer; deoxy; pH 8.4
1mbn 2.0 monomer; ferric; met
4mbn 2.0 monomer; met; supersedes 2mbn
5mbn 2.0 monomer; deoxy; supersedes 3mbn
1mbo 1.6 monomer; oxy; pH 8.4
1mbw 1.9 monomer; met; X0M & D122N mutant
Myoglobin (Sus scrofa)
1pmb 2.5 monomer - 2 chains given; aquo met
1pmbw half of coords eliminated; monomer remains
Myohemerythrin (Themiste zostericola)
2mhr 1.7/1.3 monomer; has hydrogens
Oncomodulin (Rattus norvegicus)
1omd 1.85 monomer?
Ovomucoid Third Domain (Coturnix coturnix japonica)
similar to Lophura, but not identical
1ovo 1.9 monomer, but crystallographically an octamer (a8) - 4
chains given; part of protein
1ovow made; checked -- It really looks like two tetramers -
ABGH and CDEF. N.B. C and D in the 1ovow file are NOT
the same CD as in the 1ovo file!!
Ovomucoid Third Domain (Lophura nycthemera)
similar to Coturnix, but not identical
2ovo 1.5 monomer - 1 chain given; part of protein
1-Beta-Mercaptopropionate Oxytocin (synthetic)
1xy1 1.04 monomer - 2 chains given; 8 residues; wet form; has H's
1xy2 1.20 monomer - 2 chains given; 8 residues; dry form; has H's
Avian Pancreatic Polypeptide (Meleagris gallopavo)
related to insulin and glucagon
1ppt 1.37 dimer (a2) - 1 chain given
1pptw made; checked; ok
Papain (Carica papaya)
1pad 2.8 monomer; derivative of C25; based on 8pap
2pad 2.8 monomer; derivative of C25; based on 8pap; supersedes 3pap
4pad 2.8 monomer; derivative; based on 8pap; supersedes 5pap
5pad 2.8 monomer; derivative; based on 8pap; supersedes 6pap
6pad 2.8 monomer; derivative; based on 8pap; supersedes 7pap
9pap 1.65 monomer; supersedes 8pap; Cys-25 oxidized
1ppd 2.0 monomer; 2-Hydroxyethylthiopapain; C25 inhibited
Pepsin (Sus scrofa)
Sequence is the same as pepsinogen, minus the leader peptide.
3pep 2.3 monomer
4pep 1.8 monomer; supersedes 1pep
5pep 2.34 monomer; supersedes 2pep
Pepsinogen (Sus scrofa)
Sequence is the same as pepsin, plus the leader peptide.
1psg 1.65 monomer; propeptide residues labelled 1P - 44P; may be dimer
in crystal; difficulty obtaining original literature
Phaseolin (Phaseolus vulgaris)
1phs 3.0 CA dodecamer? - 3 chains given; crystallizes as tetramer of trimers
Phosphofructokinase (Bacillus stearothermophilus)
3pfk 2.4 tetramer (a4) - 1 chain given; unliganded
3pfkw made; checked; looks ok
4pfk 2.4 tetramer (a4) - 1 chain given; complex with F6P and ADP/Mg++
5pfk 7.0 CA complex with inhibitor
Phosphofructokinase (Escherichia coli)
1pfk 2.4 tetramer (a4) - 2 chains given; complex with F1,6P and ADP/Mg++
2pfk 2.4 tetramer (a4) - 4 chains given, but 2 are part of one
tetramer & the other two are part of another; unliganded
2pfkw made; checked
Phosphoglycerate Kinase (Equus caballus)
2pgk 3.0 all residues UNK
Phosphoglycerate Kinase (Saccharomyces cerevisiae)
3pgk 2.5 monomer; complex with ATP, Mg++, and 3-Phosphoglycerate;
some crystal contacts are very close; contacts between
molecules are as close as contacts between domains
Phosphoglycerate Mutase (Saccharomyces cerevisiae)
3pgm 2.8 tetramer (a4) - 1 chain given
3pgmw made; checked
Phospholipase A2 (Bos taurus l.)
1bp2 1.7 monomer
3bp2 2.1 transaminated
Pro-Phospholipase A2 (Bos taurus l.)
2bp2 3.0 monomer; zymogen, with 7 res leader; coordinates for the
leader peptide are not included
Phospholipase A2 (Crotalus atrox)
1pp2 2.5 dimer (a2) - 2 chains given
Phospholipase A2 (Sus Scrofa)
1p2p 2.6 monomer
3p2p 2.1 mutant; surface loop deleted
Photoactive Yellow Protein (Ectothiorhodospira halophila)
1phy 2.4 CA
Photosynthetic Reaction Center (Rhodopseudomonas viridis)
1prc 2.3 tetramer (abcd) - 4 chains given; membrane protein -
solvent accessibility info will need to be re-interpreted
Plastocyanin (Populus nigra variant italica)
1pcy 1.6 monomer; Cu++; pH 6.0
2pcy 1.8 monomer; apo; pH 6.0
3pcy 1.9 monomer; Hg++
4pcy 2.15 monomer; crosslinked
5pcy 1.80 monomer; Cu+; pH 7.0
6pcy 1.90 monomer; Cu+; pH 3.8
Plastocyanin (Enteromorpha prolifera)
7pcy 1.8 monomer; hydrogens included
Poliovirus, Type I, Mahoney Strain (Homo sapiens)
2plv 2.88 240mer - 4 chains given
Prealbumin (Homo sapiens)
2pab 1.8 tetramer (a4) - 2 chains given
2pabw made acc. to file; checked
Proteinase A (Streptomyces griseus, strain K1)
2sga 1.5 monomer; sequence numbered as chymotrypsinogen - gaps;
lots of crystal contacts; phe sticking out; see MD paper
by Avbelj et al., Biochemistry 29 (1990)
1sgc 1.8 complex with chymostatin; seq numbers as for 2sga
Proteinase B (Streptomyces griseus, strain K1)
3sgb 1.8 monomer; complex with ovomucoid inhibitor; numbering has gaps
4sgb 2.1 monomer; complex with potato inhibitor; inhibitor is 51
res long -- could be used, too
Proteinase K (Tritirachium album limber)
2prk 1.5 monomer; pseudodimer in crystal
Proteinase Inhibitor IIA (Bos taurus)
1bus NMR monomer - 5 chains given
2bus NMR monomer - 1 chain given -- energy minimized structure
Pseudoazurin (Alcaligenes faecalis, strain S-6)
1paz 1.55 monomer; oxidized Cu++ at pH 6.8
2paz 2.0 monomer
Inorganic Pyrophosphatase (Saccharomyces cerevisiae)
1pyp 3.0 dimer (a2) - 1 chain given
1pypw dimerized acc to included matrix; looks ok; diff from
dimer Insight makes -- non-crystallographic symmetry
Pyruvate Kinase (Felis domestica)
1pyk 2.6 CA all residues UNK
C-H-RAS P21 Protein Catalytic Domain (Homo sapiens)
2p21 2.2 CA
3p21 2.2 CA mutant (G12V)
Rat Mast Cell Protease II (Rattus rattus)
3rp2 1.9 monomer - 2 chains given; residue numbering based on
chymotrypsin -> gaps;
3rp2w made; checked
Relaxin (Sus scrofa)
1rlx --- non-experimental; based on insulin
2rlx --- non-experimental
3rlx --- non-experimental
4rlx --- non-experimental
Retinol Binding Protein (Homo sapiens)
1rbp 2.0 monomer?
Rhinovirus 14 Coat Protein (Homo sapiens)
Icosohedral - 240mer; 4 chains given = 1 unit of icosohedron
1r08 3.0 complex with antiviral agent
1rmu 3.0 mutant of 1r08; otherwise same
2r04 3.0 supersedes 1r04; complex with antiviral agent (WIN IV);
2r06 3.0 supersedes 1r06; complex with antiviral agent (WIN VI);
2r07 3.0 supersedes 1r07; complex with antiviral agent (WIN VII);
2rm2 3.0 supersedes 1rm2; complex with antiviral agent (WIN II);
2rmu 3.0 mutant (V188L in chain 1); icosohedral;
2rr1 3.0 supersedes 1rr1; complex with antiviral agent (WIN I[R])
2rs1 3.0 supersedes 1rs1; complex with antiviral agent (WIN I[S]);
2rs3 3.0 supersedes 1rs3; complex with antiviral agent (WIN III[S]);
2rs5 3.0 supersedes 1rs5; complex with antiviral agent (WIN V[S]);
4rhv 3.0
Rhinovirus Serotype 1A Coat Protein (Homo sapiens)
Icosohedral - 240mer; 4 chains given = 1 unit of icosohedron
1r1a 3.2
Rhodanese (Bos taurus)
1rhd 2.5 monomer
Ribonuclease A (Bos taurus)
1rbb 2.5 B; 2 identical chains given
1rn3 1.45 monomer
1rns 2.0 S; single chain of 1rn3 split into 2 chains
5rsa 2.0 monomer; joint x-ray & neutron - contains hydrogens
6rsa 2.0 monomer; complex with uridine vanadate; joint x-ray & neutron
7rsa 1.26 monomer; phosphate-free; joint x-ray & neutron
1rsm 2.0 monomer; cross-linked
1srn 1.8 dimer - 2 chains given; semi-synthethic - chains are
portions of RNase A
Ribonuclease T1 (Aspergillus oryzae)
1rnt 1.9 monomer; complex with 2'guanylic acid
2rnt 1.8 monomer; complex with guanyl-2'6'-guanosine
3rnt 1.8 monomer; complex with vanadate
Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO)
(Rhodospirillum rubrum)
2rub 1.7 CA dimer - 2 chains given
Rous Sarcoma Virus Protease (Rous Sarcoma virus, strain PR-C)
2rsp 2.0 dimer (a2) - 2 chains given
Rubredoxin (Clostridium pasteurianum)
4rxn 1.2 monomer; oxidized; unconstrained; supersedes 2rxn
5rxn 1.2 monomer; oxidized; constrained; supersedes 2rxn
Rubredoxin (Desulfovibrio desulfuricans, strain 27774)
6rxn 1.5 monomer
Rubredoxin (Desulfovibrio gigas)
1rdg 1.4 monomer; oxidized
Rubredoxin (Desulfovibrio vulgaris)
3rxn 1.5 monomer
7rxn 1.5 monomer; supersedes 3rxn; Fe+++ and sulfate
Sarcoplasmic Calcium-Binding Protein (Nereis diversicolor)
1scp 3.0 CA monomer - 2 chains given
Satellite Tobacco Necrosis Virus (STNV)
2stv 2.5 60mer - 1 chain given
Scorpion Neurotoxin Variant 3 (Centruroides sculpturatus Ewing)
1sn3 1.8 monomer
Southern Bean Mosaic Virus Coat Protein (SBMV)
4sbv 2.8 540mer - 3 chains given; supersedes 3sbv
Staphylococcyl Nuclease (Staphylococcus aureus)
1snc 1.65 monomer; complex with Ca++ & inhibitor
1snm 1.74 monomer; E43D mutant; complex with Ca++ & deoxythymidine
3'5'bisphosphate
2sns 1.5 monomer; complex with 2'deoxy 3'5' diphosphothymidine;
Streptomyces Subtilisin Inhibitor (Streptomyces albogriseolus, S-3253)
2ssi 2.6 dimer (a2) - 1 chain given; supersedes 1ssi
2ssiw made; checked
Subtilisin BPN (Novo) (Bacillus amyloliquefaciens)
sequence very similar to Subtilisin Carlsberg
1sbt 2.5 monomer
2sbt 2.8 monomer
1sic 2.0 CA BPN'; complex with inhibitor; inhibitor is a dimer &
binds 2 subtilisins - 1 chain of each given
1st2 2.0 BPN'; peroxide inactivated (Mets oxidized)
2st1 1.8 BPN'
1s01 1.7 monomer; mutant (M50F, N76D, G169A, Q206C, Y217K, &
N218S); residue 206 may be persulfide
2sni 2.1 complex with chymotrypsin inhibitor (Hordeum vulgare)
Subtilisin Carlsberg (Bacillus subtilis)
sequence very similar to Subtilisin BPN (Novo)
1cse 1.2 monomer; complex with Eglin-C (Hirudo medicinalis)
1sbc 2.5 monomer
2sec 1.8 complex with N-Acetyl-Eglin-C (Hirudo medicinalis)
Cu, Zn Superoxide Dismutase (Bos taurus)
2sod 2.0 dimer (a2) - 4 chains given
2sodw made; checked
Taka-Amylase A (Aspergillus oryzae)
2taa 3.0 monomer - 1 chain given
Tendamistat (Streptomyces tendae)
2ait NMR monomer - 9 chains given; with hydrogens and hydrogen
pseudoatoms; this file messes up in Insight
3ait NMR energy minimized model using AMBER
4ait NMR energy minimized model using FANTOM
Thaumatin I (Thaumatococcus danielli Benth)
1thi 3.2 CA monomer
Thermitase (Thermoactinomyces vulgaris)
homologous to Subtilisin
1tec 2.2 monomer; complex with Eglin C (Hirudo medicinalis) (inhibitor)
Thermolysin (Bacillus thermoproteolyticus)
3tln 1.6 monomer; supersedes 1tln & 2tln
4tln 2.3 monomer; complex with Leu-Hydroxylamine
5tln 2.3 monomer; complex with inhibitor
7tln 2.3 monomer; complex with inhibitor; supersedes 6tln
1tlp 2.3 monomer; complex with phosphoramidon
1tmn 1.9 monomer; complex with inhibitor
2tmn 1.6 monomer; complex with P-Leu
3tmn 1.7 monomer; complex with Val-Trp
4tmn 1.7 monomer; complex with CBZ-PHE-P-LEU-ALA
5tmn 1.6 monomer; complex with CBZ-PGL-LEU-LEU
6tmn 1.6 monomer; complex with CBZ-PGL-OLE-LEU
7tmn --- model of substrate GLY-TPH-LEU-LEU
Thioredoxin (Escherichia coli B)
1srx 2.8 CA oxidized
1trx NMR monomer - 10 chains given; reduced
Thymidine Phosphorylase (Escherichia coli K12)
1tpt 2.8 CA dimer - 1 chain given
Tobacco Mosaic Virus (TMV vulgare strain)
2tmv 2.9 2130mer - 1 chain given; complex with RNA
Tomato Bushy Stunt Virus (TBSV)
2tbv 2.9 180mer - 3 chains given
Tonin (Rattus rattus)
related to Kallikrein
1ton 1.8 monomer
Transfer RNAs
1tn1
1tn2
1tra
2tra
3tra
4tra
4tna
Triacylglycerol Acylhydrolase (Mucor miehei)
1tgl 1.9 CA monomer
Triose Phosphate Isomerase (Gallus gallus)
1tim 2.5 dimer (a2) - 2 chains given
Triose Phosphate Isomerase (Saccharomyces cerevisiae)
2ypi 2.5 dimer - 2 chains given; complex with PGA
Tropomyosin (Oryctolagus cuniculus)
2tma 15.0 CA
Troponin (Oryctolagus cuniculus)
1tnc --- non-experimental; based on parvalbumin
Troponin C (Gallus gallus)
Sequence similar to M. gallopavo (5 residues differ)
4tnc 2.0 monomer
Troponin C (Meleagris gallopavo)
Sequence similar to G. gallus (5 residues differ)
5tnc 2.0 monomer; supersedes 2tnc
Trypsin Beta (Bos taurus)
1ntp 1.8 monomer; modified; monoisopropylphosphoryl inhibited;
neutron data
1tld 1.5 monomer; beta; pH 5.3
1tpa 1.9 monomer; anhydro; complex with inhibitor
1tpo 1.7 monomer; beta; pH 5.0
1tpp 1.4 monomer; complex with APPA
2ptc 1.9 monomer; complex with PTI; supersedes 1ptc
2ptn 1.55 monomer; orthorhombic crystal; supersedes 1ptn; 2.4 M
ammonium sulfate
3ptb 1.7 monomer; benzamidine inhibited; pH 7; supersedes 2ptb
3ptn 1.7 monomer; trigonal; 2.4 M ammonium sulfate
4ptp 1.34 monomer; diisopropylphosphoryl inhibited
Trypsin (Rattus rattus)
1trm 2.3 monomer; 2 chains given; mutant (D102N); B chain more
like native
1trmw made; checked
2trm 2.8 monomer; mutant (D102N); complex with benzamidine; pH 8
Trypsin (Streptomyces griseus, strain K1)
1sgt 1.7 monomer; sequence numbered as chymotrypsin - gaps
Trypsin Inhibitor (Bos taurus)
4pti 1.5 monomer
5pti 1.0/1.8monomer; joint x-ray & neutron - H's & D's; crystal form II
6pti 1.7 monomer; crystal form III
Trypsinogen (Bos taurus)
1tgb 1.8 monomer; CA form; trypsinogen; numbered acc. to
chymotrypsin - gaps
1tgc 1.8 monomer; 50% methanol 50% water
1tgn 1.65 monomer
1tgs 1.8 monomer; complex with inhibitor
1tgt 1.7 monomer; 173 degrees K
2tga 1.8 monomer; 2.4 M MgSulfate
2tgd 2.1 monomer; complex with inhibitor
2tgp 1.9 monomer; complex with PTI
2tgt 1.7 monomer; 103 degrees K; 70:30 = methanol:water
2tpi 2.1 monomer; complex with PTI & Ile-Val; 2.4 MgSulfate
3tpi 1.9 monomer; complex with PTI & Ile-Val
4tpi 2.2 monomer; complex with PTI analog & Val-Val
TRP Repressor (Escherichia coli)
1wrp 2.2 dimer (a2) - 1 chain given
2wrp 1.65 dimer (a2) - 1 chain given; apparent error in space group in
PDB file - should be P 21 21 2
2wrpw made; checked
3wrp 1.8 dimer (a2) - 1 chain given; apo; apparent error in space group
in PDB file - should be P 21 21 2
3wrpw made; checked
Tryptophan Synthase (Salmonella typhimurium, strain TB2211/PSTH8)
1wsy 2.5 tetramer (a2b2) - 2 chains given
1wsyw made; checked
Tumor Necrosis Factor Alpha (Homo sapiens)
1tnf 2.6 trimer (a3) - 3 chains given
Tyrosyl-Transfer-RNA Synthetase (Bacillus stearothermophilus)
2ts1 2.3 dimer (a2) - 1 chain given; supersedes 1ts1
2ts1w made; checked
3ts1 2.7 dimer (a2) - 1 chain given; complex with tyrosinyl adenylate
4ts1 2.5 dimer (a2) - 1 chain given; complex with tyrosine; 318 - 417
deleted
Ubiquitin (Homo sapiens)
1ubq 1.8 monomer
Uteroglobin (Oryctolagus cuniculus)
1utg 1.34 dimer (a2) - 1 chain given; oxidized
1utgw made; checked
2utg 1.64 dimer (a2) - 2 chains given
Wheat Germ Agglutinin (Triticum vulgaris)
Two different isolectins; they differ by 5 amino acids.
3wga 1.8 dimer - 2 chains given; isolectin 2?
7wga 2.0 dimer - 2 chains given; isolectin 1
9wga 1.8 dimer - 2 chains given; supersedes 3wga; isolectin 2; this
molecule does NOT look correct - too much empty space;
orientation of different domains seems wrong. Made dimers
by using each monomer and transforming acc to C2 matrix -
9wgaAC.pdb looks better and looks like one of dimers made by
Insight. 9wgaBD.pdb has (at least) translational problems.
Reordered lit - no good picture of real structure.
1wgc 2.2 dimer - 2 chains given; complex with N-Acetylneuraminyllactose;
isolectin 1
2wgc 2.2 dimer - 2 chains given; complex with N-Acetylneuraminyllactose;
isolectin 2
Xylose Isomerase (Arthrobacter strain B3728)
1xia 2.3 CA tetramer - 2 chains given; all residues UNK
4xia 2.3 tetramer - 2 chains given; complex with inhibitor sorbitol
5xia 2.5 tetramer - 2 chains given; complex with inhibitor xylitol
Xylose Isomerase (Streptomyces rubiginosus)
2xia 3.5 CA tetramer - 2 chains given; all residues UNK
Xylose Isomerase (Streptomyces olivochromogenes)
3xia 3.0 dimer or tetramer - 1 chain given
3xiaw made; looks like one Insight makes -- no tetrameric picture
in lit; re-ordered literature
Zinc Finger (Xenopus lavis)
1znf NMR monomer - 37 chains given; model 1 to be used for geometry
