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

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