The Anatomy & Taxonomy of Protein Structure

III. Classification Of Proteins By Patterns Of Tertiary Structure

A. Summary of the Classification System

4. Index of Proteins

[PDB (Protein Data Bank) ID codes are given here for all cases where the drawing was based on coordinates then available in the Atlas of Macromolecular Structure on Microfiche (Feldmann, 1977) or in the Protein Data Bank (Bernstein, 1977). For those drawings made from coordinates provided by the crystallographers (see acknowledgements) or for the few made from published stereo figures, the PDB code is given only where that later-deposited coordinate set is essentially the same as the one used.]

Acid proteases [1APE, 1APP] , see Rhizopuspepsin
Actinidin () [2ACT] , see Papain
Adenylate kinase () [2ADK]
Doubly wound parallel β sheet (Fig. 77)
Agglutinin, wheat germ () [2WGA]
Domains 1, 2, 3, and 4: small SS-rich (Fig. 85)
Alcohol dehydrogenase, liver () [4ADH]
Domain 1: multiple β barrel (Fig. 82)
Domain 2: classic doubly wound β sheet (Fig. 76)
Aldolase, 2-keto-3-deoxy-6-phosphogluconate () [1KGA:later reconnected] ; () [Allard, 2001; 1EUA]
Singly wound parallel β barrel? (Fig. 75)
Arabinose-binding protein () [1ABP]
Domains 1 and 2: doubly wound parallel β sheet (Fig. 77)
Aspartate aminotransferase () [1AAT]
Doubly wound parallel β sheet
Aspartate carbamoyltransferase, () [1ATC]
Regulatory domain 1: open-face β sandwich (Fig. 83)
Regulatory domain 2: open-face β sandwich (Fig. 83)
Catalytic domain 1: doubly wound parallel β sheet
Catalytic domain 2: classic doubly wound β sheet (Fig. 76)
Aspartate transaminase: see Aspartate aminotransferase
Aspartate transcarbamylase ***[()]*** , see Aspartate carbamoyltransferase
Azurin () [1AZU] , see Plastocyanin
Bacteriochlorophyll protein () [2BCL]
Open-face β sandwich (Fig. 83)
Bacteriorhodopsin, see Purple membrane protein
Bence-Jones protein, see Immunoglobulin
Calcium-binding protein, carp muscle () [1CPV]
Miscellaneous antiparallel α (Fig. 74)
Carbonate dehydratase, see Carbonic anhydrase
Carbonic anhydrase C () [1CAC]
Miscellaneous parallel α/β (Fig. 78)
Carboxypeptidase A () [1CPA]
Miscellaneous parallel α/β (Fig. 78)
Catalase () [4CAT]
Domain 1: up-and-down β barrel
Domain 2: miscellaneous antiparallel α
Domain 3: doubly wound parallel β sheet
Chymotrypsin () [2CHA] , see Trypsin
Citrate synthase () [1CTS]
Miscellaneous antiparallel α
Concanavalin A () [2CNA]
Jellyroll Greek key β barrel (Fig. 81)
Crambin () [1CRN]
Small SS-rich (Fig. 85)
γ-Crystallin () [1GCR]
Domains 1 and 2: jellyroll Greek key β barrel
Cytochrome b5 () [2B5C]
Small metal-rich (Fig. 86)
Cytochrome b562 () [156B]
Up-and-down helix bundle (Fig. 72)
Cytochrome c () [4CYT]
Small metal-rich (Fig. 86)
Cytochrome c′ () [1CCY]
Up-and-down helix bundle (Fig. 72)
Cytochrome c2 () [1C2C] , see Cytochrome c
Cytochrome c3 () [1CY3]
Small metal-rich (Fig. 86)
Cytochrome c550 () [155C] , see Cytochrome c
Cytochrome c551 (), [251C] see Cytochrome c
Cytochrome c555 (), see Cytochrome c
Cytochrome c peroxidase () [2CYP]
Domain 1: Greek key helix bundle
Domain 2: miscellaneous antiparallel α
Dehydrogenases, see Alcohol, Glyceraldehyde phosphate, Malate, or Lactate
Dihydrofolate reductase () [2DFR]
Doubly wound parallel β sheet (Fig. 77)
Elastase () [1EST] , see Trypsin
Erabutoxin ()
Small SS-rich (Fig. 85)
Ferredoxin () [1FDX]
Small metal-rich (Fig. 86)
Ferritin (; )
Up-and-down helix bundle
Flavodoxin () [4FXN]
Doubly wound parallel β sheet (Fig. 77)
Gene 5 protein, fd phage () [strand connectivity changed-2GN5, 1VQB]
Miscellaneous antiparallel β
Glucosephosphate isomerase () [1PGI]
Domains 1 and 2: miscellaneous parallel α/β
Glutathione peroxidase ()
Doubly wound parallel β sheet
Glutathione reductase () [1GRS]
Domains 1 and 2: doubly wound parallel β sheet (Fig. 77)
Domain 3: open-face β sandwich (Fig. 83)
Glyceraldehyde-phosphate dehydrogenase () [1GPD]
Domain 1: doubly wound parallel β sheet (Fig. 77)
Domain 2: open-face β sandwich (Fig. 83)
Glycogen phosphorylase ()
Domain 1: doubly wound parallel β sheet, five-layer
Domain 2: classic doubly wound β sheet, five-layer (Fig. 76)
Hemagglutinin, influenza virus () [1HMG]
HA1: jellyroll Greek key β barrel
HA2: open-face β sandwich
HA2 around 3-fold: miscellaneous helix cluster
Hemerythrin () [1HMN] , see Myohemerythrin
Hemoglobin () [2MHB]
Greek key helix bundle (Fig. 73)
Hexokinase () [2YHX]
Domains 1 and 2: doubly wound parallel β sheet (Fig. 77)
High-potential iron protein () [1HIP]
Small metal-rich (Fig. 86)
ρ-Hydroxybenzoate hydroxylase (4-hydroxybenzoate 3-mono-oxygenase) ) [1PHH]
Domain 1: doubly wound parallel β sheet
Domain 2: open-face β sandwich
Domain 3: miscellaneous antiparallel α
Immunoglobulin (; ) [1REI, 2FAB]
Variable and constant domains: Greek key β barrel (Fig. 80)
Insulin () [1INS]
Small SS-rich (Fig. 85)
Kinases, see Adenylate kinase, Hexokinase, Phosphoglycerate kinase, Phosphofructokinase, or Pyruvate kinase
Lactate dehydrogenase () [4LDH]
Domain 1: classic doubly wound β sheet (Fig. 76)
Domain 2: miscellaneous antiparallel β (Fig. 84)
Lysozyme, hen egg white () [1LYZ]
Miscellaneous antiparallel α (Fig. 73)
Lysozyme, T4 phage () [1LZM]
Domain 1: open-face β sandwich (Fig. 83)
Domain 2: Greek key helix bundle (Fig. 73)
L7/L12 ribosomal protein () [1CTF]
Open-face β sandwich
Malate dehydrogenase () [1MDH] , see Lactate dehydrogenase
Myoglobin () [1MBN] , see Hemoglobin
Myohemerythrin () [1MHR]
Up-and-down helix bundle (Fig. 72)
Neurotoxin
Cobra (), see Erabutoxin
Sea snake () [1NXB] , see Erabutoxin
Nuclease, staphylococcal (or micrococcal) () [1SNS]
Greek key β barrel (Fig. 80)
Papain () [8PAP]
Domain 1: Greek key helix bundle (Fig. 73)
Domain 2: up-and-down β barrel (Fig. 79)
Parvalbumin, see Calcium-binding protein
Pepsin () [1PEP] , see Rhizopuspepsin
Plastocyanin () [1PCY]
Greek key β barrel (Fig. 80)
Phosphoglycerate kinase () [2PGK]
Domain 1: doubly wound parallel β sheet
Domain 2: classic doubly wound β sheet (Fig. 76)
Phosphoglycerate mutase () [1PGM]
Doubly wound parallel β sheet (Fig. 77)
Phospholipase A2 () [1BP2]
Small SS-rich (Fig. 85)
Phosphorylase, see Glycogen phosphorylase
Prealbumin () [2PAB]
Greek key β barrel (Fig. 80)
Protein A fragment, staphylococcal () [1FC2]
Up-and-down helix bundle (Fig. 72)
Purple membrane protein () [1BRD, 1MOM]
Either up-and-down or Greek key helix bundle [up & down]
Pyruvate kinase () [1PYK]
Domain 1: singly wound parallel β barrel (Fig. 75)
Domain 2: Greek key β barrel (Fig. 80)
Domain 3: doubly wound parallel β sheet (Fig. 77)
Rhodanese () [1RHD]
Domains 1 and 2: doubly wound parallel β sheet (Fig. 77)
Rhizopuspepsin () [1APR]
Domains 1 and 2: other β barrel (Fig. 82)
Ribonuclease, bovine pancreatic () [1RNS]
Partial β barrel (Fig. 82)
Rubredoxin () [3RXN]
Small metal-rich (Fig. 86)
Serine proteases, see Trypsin, Chymotrypsin, Elastase, Streptomyces griseus proteases A and B, or Subtilisin
Southern bean mosaic virus protein () [1SBV]
Jellyroll Greek key β barrel (Fig. 81)
Streptomyces griseus protease A () [1SGA] , see Trypsin
Streptomyces griseus protease B () [1SGB] , see Trypsin
Subtilisin () [1SBT]
Doubly wound parallel β sheet (Fig. 77)
Subtilisin inhibitor, Streptomyces () [2SSI]
Open-face β sandwich (Fig. 83)
Sulfhydryl proteases, see Actinidin, Papain
Superoxide dismutase, Cu,Zn () [2SOD]
Greek key β barrel (Fig. 80)
Thermolysin () [2TLN]
Domain 1: open-face β sandwich (Fig. 83)
Domain 2: Greek key helix bundle (Fig. 83)
Thioredoxin, E. coli () [1SRX]
Miscellaneous parallel α/β (Fig. 78)
Thiosulfate sulfurtransferase, see Rhodanese
Tobacco mosaic virus protein ()
Up-and-down helix bundle (Fig. 72)
Tomato bushy stunt virus protein () [2TBV]
"Domain" 1: miscellaneous antiparallel β (Fig. 84)
Domains 2 and 3: jellyroll Greek key β barrel (Fig. 81)
Triosephosphate isomerase () [1TIM]
Singly wound parallel β barrel (Fig. 75)
tRNA synthetase, tyrosyl (; D. M. Blow, personal communication)
Domain 1: classic doubly wound β sheet
Domain 2: up-and-down helix bundle
Trypsin ()
Domains 1 and 2: Greek key β barrel (Fig. 80)
Trypsin inhibitor, pancreatic () [3PTI]
Small SS-rich (Fig. 85)
Trypsin inhibitor, soybean ()
Up-and-down β barrel (Fig. 79)
Uteroglobin ()
Up-and-down helix bundle (Fig. 72)
Viral coat proteins, see Southern bean mosaic virus, Tobacco mosaic virus, or Tomato bushy stunt virus