The Anatomy & Taxonomy of Protein Structure 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 (Baker, 1980) [2ACT] , see Papain
Adenylate kinase (Schulz et al., 1974a) [2ADK]
Doubly wound parallel β sheet (Fig. 77)
Agglutinin, wheat germ (Wright, 1977) [2WGA]
Domains 1, 2, 3, and 4: small SS-rich (Fig. 85)
Alcohol dehydrogenase, liver (Eklund et al., 1976) [4ADH]
Domain 1: multiple β barrel (Fig. 82)
Domain 2: classic doubly wound β sheet (Fig. 76)
Aldolase, 2-keto-3-deoxy-6-phosphogluconate (Mavridis and Tulinsky, 1976) [1KGA:later reconnected] ; (Richardson, 1979) [Allard, 2001; 1EUA]
Singly wound parallel β barrel? (Fig. 75)
Arabinose-binding protein (Quiocho et al., 1977) [1ABP]
Domains 1 and 2: doubly wound parallel β sheet (Fig. 77)
Aspartate aminotransferase (Ford et al., 1980) [1AAT]
Doubly wound parallel β sheet
Aspartate carbamoyltransferase, (Monaco et al., 1978) [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 ***[(Monaco et al., 1978)]*** , see Aspartate carbamoyltransferase
Azurin (Adman et al., 1978) [1AZU] , see Plastocyanin
Bacteriochlorophyll protein (B. W. Matthews et al., 1979) [2BCL]
Open-face β sandwich (Fig. 83)
Bacteriorhodopsin, see Purple membrane protein
Bence-Jones protein, see Immunoglobulin
Calcium-binding protein, carp muscle (Kretsinger and Nockolds, 1973) [1CPV]
Miscellaneous antiparallel α (Fig. 74)
Carbonate dehydratase, see Carbonic anhydrase
Carbonic anhydrase C (Lindskog et al., 1971) [1CAC]
Miscellaneous parallel α/β (Fig. 78)
Carboxypeptidase A (Quiocho and Lipscomb, 1971) [1CPA]
Miscellaneous parallel α/β (Fig. 78)
Catalase (Vainshtein et al., 1980) [4CAT]
Domain 1: up-and-down β barrel
Domain 2: miscellaneous antiparallel α
Domain 3: doubly wound parallel β sheet
Chymotrypsin (Birktoft and Blow, 1972) [2CHA] , see Trypsin
Citrate synthase (Wiegand et al., 1979) [1CTS]
Miscellaneous antiparallel α
Concanavalin A (Reeke et al., 1975) [2CNA]
Jellyroll Greek key β barrel (Fig. 81)
Crambin (Hendrickson and Teeter, 1981) [1CRN]
Small SS-rich (Fig. 85)
γ-Crystallin (Blundell et al., 1981) [1GCR]
Domains 1 and 2: jellyroll Greek key β barrel
Cytochrome b5 (Mathews et al., 1972) [2B5C]
Small metal-rich (Fig. 86)
Cytochrome b562 (Mathews et al., 1979) [156B]
Up-and-down helix bundle (Fig. 72)
Cytochrome c (Swanson et al., 1977) [4CYT]
Small metal-rich (Fig. 86)
Cytochrome c′ (Weber et al., 1980) [1CCY]
Up-and-down helix bundle (Fig. 72)
Cytochrome c2 (Salemme et al., 1973) [1C2C] , see Cytochrome c
Cytochrome c3 (Haser et al., 1979) [1CY3]
Small metal-rich (Fig. 86)
Cytochrome c550 (Timkovich and Dickerson, 1973) [155C] , see Cytochrome c
Cytochrome c551 (Almassy and Dickerson, 1978), [251C] see Cytochrome c
Cytochrome c555 (Korszun and Salemme, 1977), see Cytochrome c
Cytochrome c peroxidase (Poulos et al., 1980) [2CYP]
Domain 1: Greek key helix bundle
Domain 2: miscellaneous antiparallel α
Dehydrogenases, see Alcohol, Glyceraldehyde phosphate, Malate, or Lactate
Dihydrofolate reductase (Matthews et al., 1977) [2DFR]
Doubly wound parallel β sheet (Fig. 77)
Elastase (Sawyer et al., 1978) [1EST] , see Trypsin
Erabutoxin (Low et al., 1976)
Small SS-rich (Fig. 85)
Ferredoxin (Adman et al., 1973) [1FDX]
Small metal-rich (Fig. 86)
Ferritin (Banyard et al., 1978; Clegg et al., 1980)
Up-and-down helix bundle
Flavodoxin (Burnett et al., 1974) [4FXN]
Doubly wound parallel β sheet (Fig. 77)
Gene 5 protein, fd phage (McPherson et al., 1979) [strand connectivity changed-2GN5, 1VQB]
Miscellaneous antiparallel β
Glucosephosphate isomerase (Shaw and Muirhead, 1977) [1PGI]
Domains 1 and 2: miscellaneous parallel α/β
Glutathione peroxidase (Ladenstein et al., 1979)
Doubly wound parallel β sheet
Glutathione reductase (Schulz et al., 1978) [1GRS]
Domains 1 and 2: doubly wound parallel β sheet (Fig. 77)
Domain 3: open-face β sandwich (Fig. 83)
Glyceraldehyde-phosphate dehydrogenase (Buehner et al., 1974) [1GPD]
Domain 1: doubly wound parallel β sheet (Fig. 77)
Domain 2: open-face β sandwich (Fig. 83)
Glycogen phosphorylase (Sprang and Fletterick, 1979)
Domain 1: doubly wound parallel β sheet, five-layer
Domain 2: classic doubly wound β sheet, five-layer (Fig. 76)
Hemagglutinin, influenza virus (Wilson et al., 1981) [1HMG]
HA1: jellyroll Greek key β barrel
HA2: open-face β sandwich
HA2 around 3-fold: miscellaneous helix cluster
Hemerythrin (Stenkamp et al., 1978) [1HMN] , see Myohemerythrin
Hemoglobin (Ladner et al., 1977) [2MHB]
Greek key helix bundle (Fig. 73)
Hexokinase (Steitz et al., 1976) [2YHX]
Domains 1 and 2: doubly wound parallel β sheet (Fig. 77)
High-potential iron protein (Carter et al., 1974) [1HIP]
Small metal-rich (Fig. 86)
ρ-Hydroxybenzoate hydroxylase (4-hydroxybenzoate 3-mono-oxygenase) Wierenga et al., 1979) [1PHH]
Domain 1: doubly wound parallel β sheet
Domain 2: open-face β sandwich
Domain 3: miscellaneous antiparallel α
Immunoglobulin (Epp et al., 1974; Silverton et al., 1977) [1REI, 2FAB]
Variable and constant domains: Greek key β barrel (Fig. 80)
Insulin (Blundell et al., 1972) [1INS]
Small SS-rich (Fig. 85)
Kinases, see Adenylate kinase, Hexokinase, Phosphoglycerate kinase, Phosphofructokinase, or Pyruvate kinase
Lactate dehydrogenase (Adams et al., 1970) [4LDH]
Domain 1: classic doubly wound β sheet (Fig. 76)
Domain 2: miscellaneous antiparallel β (Fig. 84)
Lysozyme, hen egg white (Imoto et al., 1972) [1LYZ]
Miscellaneous antiparallel α (Fig. 73)
Lysozyme, T4 phage (Matthews and Remington, 1974) [1LZM]
Domain 1: open-face β sandwich (Fig. 83)
Domain 2: Greek key helix bundle (Fig. 73)
L7/L12 ribosomal protein (Leijonmarck et al., 1980) [1CTF]
Open-face β sandwich
Malate dehydrogenase (Hill et al., 1972) [1MDH] , see Lactate dehydrogenase
Myoglobin (Watson, 1969) [1MBN] , see Hemoglobin
Myohemerythrin (Hendrickson and Ward, 1977) [1MHR]
Up-and-down helix bundle (Fig. 72)
Neurotoxin
Cobra (Walkinshaw et al., 1980), see Erabutoxin
Sea snake (Tsernoglou and Petsko, 1977) [1NXB] , see Erabutoxin
Nuclease, staphylococcal (or micrococcal) (Arnone et al., 1971) [1SNS]
Greek key β barrel (Fig. 80)
Papain (Drenth et al., 1971) [8PAP]
Domain 1: Greek key helix bundle (Fig. 73)
Domain 2: up-and-down β barrel (Fig. 79)
Parvalbumin, see Calcium-binding protein
Pepsin (Andreeva and Gustchina, 1979) [1PEP] , see Rhizopuspepsin
Plastocyanin (Colman et al., 1978) [1PCY]
Greek key β barrel (Fig. 80)
Phosphoglycerate kinase (Banks et al., 1979) [2PGK]
Domain 1: doubly wound parallel β sheet
Domain 2: classic doubly wound β sheet (Fig. 76)
Phosphoglycerate mutase (Campbell et al., 1974) [1PGM]
Doubly wound parallel β sheet (Fig. 77)
Phospholipase A2 (Dijkstra et al., 1978) [1BP2]
Small SS-rich (Fig. 85)
Phosphorylase, see Glycogen phosphorylase
Prealbumin (Blake et al., 1978) [2PAB]
Greek key β barrel (Fig. 80)
Protein A fragment, staphylococcal (Deisenhofer et al., 1978) [1FC2]
Up-and-down helix bundle (Fig. 72)
Purple membrane protein (Henderson and Unwin, 1975) [1BRD, 1MOM]
Either up-and-down or Greek key helix bundle [up & down]
Pyruvate kinase (Stuart et al., 1979) [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 (Ploegman et al., 1978) [1RHD]
Domains 1 and 2: doubly wound parallel β sheet (Fig. 77)
Rhizopuspepsin (Subramanian et al., 1977) [1APR]
Domains 1 and 2: other β barrel (Fig. 82)
Ribonuclease, bovine pancreatic (Wyckoff et al., 1970) [1RNS]
Partial β barrel (Fig. 82)
Rubredoxin (Watenpaugh et al., 1979) [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 (Abad-Zapatero et al., 1980) [1SBV]
Jellyroll Greek key β barrel (Fig. 81)
Streptomyces griseus protease A (Brayer et al., 1978) [1SGA] , see Trypsin
Streptomyces griseus protease B (Delbaere et al., 1975) [1SGB] , see Trypsin
Subtilisin (Wright et al., 1969) [1SBT]
Doubly wound parallel β sheet (Fig. 77)
Subtilisin inhibitor, Streptomyces (Mitsui et al., 1979) [2SSI]
Open-face β sandwich (Fig. 83)
Sulfhydryl proteases, see Actinidin, Papain
Superoxide dismutase, Cu,Zn (Richardson et al., 1975) [2SOD]
Greek key β barrel (Fig. 80)
Thermolysin (Colman et al., 1972) [2TLN]
Domain 1: open-face β sandwich (Fig. 83)
Domain 2: Greek key helix bundle (Fig. 83)
Thioredoxin, E. coli (Holmgren et al., 1975) [1SRX]
Miscellaneous parallel α/β (Fig. 78)
Thiosulfate sulfurtransferase, see Rhodanese
Tobacco mosaic virus protein (Bloomer et al., 1978)
Up-and-down helix bundle (Fig. 72)
Tomato bushy stunt virus protein (Harrison et al., 1978) [2TBV]
"Domain" 1: miscellaneous antiparallel β (Fig. 84)
Domains 2 and 3: jellyroll Greek key β barrel (Fig. 81)
Triosephosphate isomerase (Banner et al., 1975) [1TIM]
Singly wound parallel β barrel (Fig. 75)
tRNA synthetase, tyrosyl (Irwin et al., 1976; D. M. Blow, personal communication)
Domain 1: classic doubly wound β sheet
Domain 2: up-and-down helix bundle
Trypsin (Stroud et al., 1974)
Domains 1 and 2: Greek key β barrel (Fig. 80)
Trypsin inhibitor, pancreatic (Deisenhofer and Steigemann, 1975) [3PTI]
Small SS-rich (Fig. 85)
Trypsin inhibitor, soybean (Sweet et al., 1974)
Up-and-down β barrel (Fig. 79)
Uteroglobin (Mornon et al., 1980)
Up-and-down helix bundle (Fig. 72)
Viral coat proteins, see Southern bean mosaic virus, Tobacco mosaic virus, or Tomato bushy stunt virus