Folds:

1. c.1: TIM beta/alpha-barrel [51350] (26 superfamilies) contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 the first seven superfamilies have similar phosphate-binding sites

2. c.2: NAD(P)-binding Rossmann-fold domains [51734] (1 superfamily) core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456 The nucleotide-binding modes of this and the next two folds/superfamilies are similar

3. c.3: FAD/NAD(P)-binding domain [51904] (1 superfamily) core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander

4. c.4: Nucleotide-binding domain [51970] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like

5. c.5: MurCD N-terminal domain [51983] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group

6. c.6: Cellulases [51988] (1 superfamily) variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567

7. c.7: PFL-like glycyl radical enzymes [51997] (1 superfamily) contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel

8. c.8: The "swivelling" beta/beta/alpha domain [52008] (6 superfamilies) 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology this domain is thought to be mobile in all proteins known to contain it

9. c.9: Barstar-like [52037] (2 superfamilies) 2 layers, a/b; parallel beta-sheet of 3 strands, order 123

10. c.10: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) [52046] (2 superfamilies) 2 curved layers, a/b; parallel beta-sheet; order 1234...N

11. c.11: Outer arm dynein light chain 1 [52074] (1 superfamily) (beta-beta-alpha)n superhelix

12. c.12: Ribosomal proteins L15p and L18e [52079] (1 superfamily) core: three turns of irregular (beta-beta-alpha)n superhelix

13. c.13: SpoIIaa-like [52086] (2 superfamilies) core: 4 turns of a (beta-alpha)n superhelix

14. c.14: ClpP/crotonase [52095] (1 superfamily) core: 4 turns of (beta-beta-alpha)n superhelix

15. c.15: BRCT domain [52112] (1 superfamily) 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134

16. c.16: Lumazine synthase [52120] (1 superfamily) 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134

17. c.17: Caspase-like [52128] (1 superfamily) 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134

18. c.18: DNA glycosylase [52140] (1 superfamily) 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134

19. c.19: FabD/lysophospholipase-like [52150] (1 superfamily) core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest

20. c.20: Initiation factor IF2/eIF5b, domain 3 [52155] (1 superfamily) 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134

21. c.21: Ribosomal protein L13 [52160] (1 superfamily) 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214

22. c.22: Ribosomal protein L4 [52165] (1 superfamily) 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423

23. c.23: Flavodoxin-like [52171] (16 superfamilies) 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345

24. c.24: Methylglyoxal synthase-like [52334] (1 superfamily) 3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145

25. c.25: Ferredoxin reductase-like, C-terminal NADP-linked domain [52342] (1 superfamily) 3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145

26. c.26: Adenine nucleotide alpha hydrolase-like [52373] (3 superfamilies) core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145

27. c.27: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52417] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like

28. c.28: Cryptochrome/photolyase, N-terminal domain [52424] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like

29. c.30: PreATP-grasp domain [52439] (1 superfamily) 3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands possible rudiment form of Rossmann-fold domain

30. c.31: DHS-like NAD/FAD-binding domain [52466] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like

31. c.32: Tubulin, GTPase domain [52489] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456

32. c.33: Cysteine hydrolase [52498] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456

33. c.34: DFP DNA/pantothenate metabolism flavoprotein [52506] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456

34. c.35: Phosphosugar isomerase [52511] (1 superfamily) core: 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456

35. c.36: Thiamin diphosphate-binding fold (THDP-binding) [52517] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465

36. c.37: P-loop containing nucleotide triphosphate hydrolases [52539] (1 superfamily) 3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes

37. c.38: Fructose permease, subunit IIb [52727] (1 superfamily) 3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156

38. c.39: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52732] (1 superfamily) 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567

39. c.40: Methylesterase CheB, C-terminal domain [52737] (1 superfamily) 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567

40. c.41: Subtilisin-like [52742] (1 superfamily) 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3

41. c.42: Arginase/deacetylase [52767] (1 superfamily) 3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456

42. c.43: CoA-dependent acyltransferases [52776] (1 superfamily) core: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest

43. c.44: Phosphotyrosine protein phosphatases I-like [52787] (2 superfamilies) 3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134

44. c.45: (Phosphotyrosine protein) phosphatases II [52798] (1 superfamily) core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1432

45. c.46: Rhodanese/Cell cycle control phosphatase [52820] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451

46. c.47: Thioredoxin fold [52832] (2 superfamilies) core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest

47. c.48: TK C-terminal domain-like [52921] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallel to the rest

48. c.49: Pyruvate kinase C-terminal domain-like [52934] (2 superfamilies) 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest

49. c.50: Leucine aminopeptidase (Aminopeptidase A), N-terminal domain [52948] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 23145; strand 2 is antiparallel to the rest

50. c.51: Anticodon-binding domain-like [52953] (4 superfamilies) 3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 is antiparallel to the rest

51. c.52: Restriction endonuclease-like [52979] (3 superfamilies) core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest

52. c.53: Resolvase-like [53040] (2 superfamilies) Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest

53. c.54: IIA domain of mannose transporter, IIA-Man [53061] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest

54. c.55: Ribonuclease H-like motif [53066] (7 superfamilies) 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest

55. c.56: Phosphorylase/hydrolase-like [53162] (6 superfamilies) core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops

56. c.57: Molybdenum cofactor biosynthesis proteins [53217] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold

57. c.58: Aminoacid dehydrogenase-like, N-terminal domain [53222] (1 superfamily) core: 3 layers: a/b/a; parallel beta-sheet of 4 strands; 2134

58. c.59: MurD-like peptide ligases, peptide-binding domain [53243] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest

59. c.60: Phosphoglycerate mutase-like [53253] (1 superfamily) core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 is antiparallel to the rest

60. c.61: PRTase-like [53270] (1 superfamily) core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest

61. c.62: vWA-like [53299] (1 superfamily) core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest

62. c.63: CoA transferase [53315] (1 superfamily) core: 3 layers: a/b/a; beta-sheet of 7 strands, order 4321567; part of sheet is folded upon itself and forms a barrel-like structure

63. c.64: Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53322] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 6 strands, order 231456; strand 3 is antiparallel to the rest

64. c.65: Formyltransferase [53327] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest

65. c.66: S-adenosyl-L-methionine-dependent methyltransferases [53334] (1 superfamily) core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest

66. c.67: PLP-dependent transferases [53382] (1 superfamily) main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest

67. c.68: Nucleotide-diphospho-sugar transferases [53447] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest

68. c.69: alpha/beta-Hydrolases [53473] (1 superfamily) core: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest

69. c.70: Nucleoside hydrolase [53589] (1 superfamily) core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest

70. c.71: Dihydrofolate reductases [53596] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 34251687; strand 8 is antiparallel to the rest

71. c.72: Ribokinase-like [53612] (2 superfamilies) core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest potential superfamily: members of this fold have similar functions but different ATP-binding sites

72. c.73: Carbamate kinase-like [53632] (1 superfamily) 3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest

73. c.74: AraD-like aldolase/epimerase [53638] (1 superfamily) 3 layers: a/b/a; mixed (mostly antiparallel) beta-sheet of 9 strands, order 432159876; left-handed crossover between strands 4 and 5

74. c.76: Alkaline phosphatase-like [53648] (1 superfamily) core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest

75. c.77: Isocitrate/Isopropylmalate dehydrogenases [53658] (1 superfamily) consists of two intertwined (sub)domains related by pseudodyad; duplication 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest

76. c.78: ATC-like [53670] (2 superfamilies) consists of two similar domains related by pseudodyad; duplication core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134

77. c.79: Tryptophan synthase beta subunit-like PLP-dependent enzymes [53685] (1 superfamily) consists of two similar domains related by pseudodyad; duplication core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214

78. c.80: SIS domain [53696] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345

79. c.81: Formate dehydrogenase/DMSO reductase, domains 1-3 [53705] (1 superfamily) contains of two similar intertwined domains related by pseudodyad; duplication core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451

80. c.82: ALDH-like [53719] (1 superfamily) consists of two similar domains with 3 layers (a/b/a) each; duplication core: parallel beta-sheet of 5 strands, order 32145

81. c.83: Aconitase iron-sulfur domain [53731] (1 superfamily) consists of three similar domains with 3 layers (a/b/a) each; duplication core: parallel beta-sheet of 5 strands, order 32145

82. c.84: Phosphoglucomutase, first 3 domains [53737] (1 superfamily) consists of three similar domains with 3 layers (a/b/a) each; duplication core: mixed beta-sheet of 4 strands, order 2134, strand 4 is antiparallel to the rest

83. c.85: L-fucose isomerase, N-terminal and second domains [53742] (1 superfamily) consists of two domains of similar topology, 3 layers (a/b/a) each Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345 Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134

84. c.86: Phosphoglycerate kinase [53747] (1 superfamily) consists of two non-similar domains, 3 layers (a/b/a) each Domain 1 has parallel beta-sheet of 6 strands, order 342156 Domain 2 has parallel beta-sheet of 6 strands, order 321456

85. c.87: UDP-Glycosyltransferase/glycogen phosphorylase [53755] (1 superfamily) consists of two non-similar domains with 3 layers (a/b/a) each domain 1: parallel beta-sheet of 7 strands, order 3214567 domain 2: parallel beta-sheet of 6 strands, order 321456

86. c.88: Glutaminase/Asparaginase [53773] (1 superfamily) consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5 Domain 2 has parallel beta-sheet of 4 strands, order 1234

87. c.89: Phosphofructokinase [53783] (1 superfamily) consists of two non-similar domains, 3 layers (a/b/a) each Domain 1 has mixed sheet of 7 strands, order 3214567; strands 3 & 7 are antiparallel to the rest Domain 2 has parallel sheet of 4 strands, order 2314

88. c.90: Cobalt precorrin-4 methyltransferase CbiF [53789] (1 superfamily) consists of two non-similar domains Domain 1 has parallel sheet of 5 strands, order 32415 Domain 2 has mixed sheet of 5 strands, order 12534; strands 4 & 5 are antiparallel to the rest

89. c.91: PEP carboxykinase-like [53794] (1 superfamily) contains a P-loop NTP-binding motif; mixed beta-sheet folds into a barrel-like structure with helices packed on one side

90. c.92: Chelatase-like [53799] (2 superfamilies) duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134

91. c.93: Periplasmic binding protein-like I [53821] (1 superfamily) consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication parallel beta-sheet of 6 strands, order 213456

92. c.94: Periplasmic binding protein-like II [53849] (1 superfamily) consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest

93. c.95: Thiolase-like [53900] (1 superfamily) consists of two similar domains related by pseudodyad; duplication 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strands 1 & 5 are antiparallel to the rest

94. c.96: Fe-only hydrogenase [53919] (1 superfamily) consist of two intertwined domains; contains partial duplication

95. c.97: Cytidine deaminase-like [53926] (2 superfamilies) core: alpha-beta(2)-(alpha-beta)2; 3 layers (a/b/a); mixed beta-sheet of 4 strands, order 2134; strand 2 is antiparallel to the rest

96. c.98: MurF and HprK N-domain-like [63417] (2 superfamilies) core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1234; structural similarity of the MurF and HprK extends beyond the core.

97. c.99: Dipeptide transport protein [63991] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; also contains a C-terminal alpha+beta subdomain

98. c.100: Thiamin pyrophosphokinase, catalytic domain [63998] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 432156

99. c.101: Undecaprenyl diphosphate synthase [64004] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 342156

100. c.102: Cell-division inhibitor MinC, N-terminal domain [64042] (1 superfamily) beta(2)-(alpha-beta)2-beta; 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 1 & 5 are antiparallel to the rest

101. c.103: Hypothetical protein MT938 (MTH938) [64075] (1 superfamily) core: 3 layers, b+a/b/a ; the central mixed sheet of 5 strands: order 21534; strand 2 is antiparallel to the rest

102. c.104: YjeF N-terminal domain-like [64152] (1 superfamily) 3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 32145678; strand 8 is antiparallel to the rest

103. c.105: 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64157] (1 superfamily) core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 45321678, strands 4 and 5 are antiparallel to the rest

104. c.106: SurE-like [64166] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 9 strands, order 342156798; strands 3, 8 and 9 are antiparallel to the rest; left-handed crossover connection between strands 6 and 7

105. c.107: DHH phosphoesterases [64181] (1 superfamily) consists of two non-similar domains Domain 1 has parallel sheet of 6 strands, order 321456 Domain 2 has mixed sheet of 5 strands, order 12345; strands 1 & 4 are antiparallel to the rest

106. c.108: HAD-like [56783] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456

107. c.109: PEP carboxykinase N-terminal domain [68922] (1 superfamily) contains mixed beta-sheets; topology is partly similar to that of the catalytic C-terminal domain

108. c.110: D-Tyr tRNAtyr deacylase [69499] (1 superfamily) beta(2)-(alpha-beta)2-beta(3); 3 layers, a/b/b; some topological similarity to the N-terminal domain of MinC

109. c.111: Molybdenum cofactor biosynthesis protein MoeB [69571] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 are antiparallel to the rest

110. c.112: Glycerol-3-phosphate (1)-acyltransferase [69592] (1 superfamily) 3 layers: a/b/a; mixed beta-sheet of 9 strands, order 918736452; strands 1, 2 and 8 are antiparallel to the rest

111. c.113: Uroporphyrinogen III synthase (U3S, HemD) [69617] (1 superfamily) duplication: consists of two similar 'swapped' domain with 3 layers (a/b/a) each; parallel beta-sheet of 5 strands, order 21345

112. c.114: YchN-like [75168] (1 superfamily) 3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 43215

113. c.115: Hypothetical protein MTH777 (MT0777) [75180] (1 superfamily) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456

114. c.116: alpha/beta knot [75216] (1 superfamily) core: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deep trefoil knot

115. c.117: Amidase signature (AS) enzymes [75303] (1 superfamily) possible duplication: the topologies of N- and C-terminal halves are similar; 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213549A867 (A=10); strands from 5 to 9 are antiparallel to the rest

116. c.118: Putative glycerate kinase (hypothetical protein TM1585) [82543] (1 superfamily) consists of two non-similar domains Domain 1 has parallel sheet of 6 strands, order 321456, Rossmann-like topology Domain 2 has mixed sheet of 6 strands, order 126345; strands 5 and 6 are antiparallel to the rest; some similarity to CbiF Domain 2

117. c.119: DegV-like [82548] (1 superfamily) consists of two non-similar domains Domain 1 has parallel sheet of 5 strands, order 21345, and antiparallel 3-stranded sheet, 132 Domain 2 has mixed sheet of 6 strands, order 321645; strands 2 and 6 are antiparallel to the rest

More info for Class c: Alpha and beta proteins (a/b)

Timeline for Class c: Alpha and beta proteins (a/b):

• Class c: Alpha and beta proteins (a/b) first appeared (with stable ids) in SCOP 1.55
  
• Class c: Alpha and beta proteins (a/b) appears in SCOP 1.61
  
• Class c: Alpha and beta proteins (a/b) appears in SCOP 1.65
  
• Class c: Alpha and beta proteins (a/b) appears in the current release, SCOPe 2.08