Structural Classification of Proteins
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Class: Alpha and beta proteins (a+b)

Mainly antiparallel beta sheets (segregated alpha and beta regions)

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a+b)
    Mainly antiparallel beta sheets (segregated alpha and beta regions)

Folds:

  1. Microbial ribonucleases (1)
    single helix packs against antiparallel beta-sheet
    1. Microbial ribonucleases (1) pic
  2. Lysozyme-like (1)
    common alpha+beta motif for the active site region
    1. Lysozyme-like (7)
  3. Cysteine proteinases (1)
    consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
    1. Cysteine proteinases (7) pic
      the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet
  4. His-Me finger endonucleases (1)
    core: (alpha)-beta-omega_loop-beta-alpha; embeded in larger different structures
    1. His-Me finger endonucleases (4)
      common motif contains conserved histidine residue and metal-binding site
  5. RNase A-like (1)
    contains long curved beta-sheet and 3 helices
    1. RNase A-like (1) pic
      can be classified as disulphide-rich
  6. Prion protein domain (1)
    beta-alpha-beta-alpha(2); antiparallel beta-ribbon
    1. Prion protein domain (1)
  7. LysM domain (1)
    beta-alpha(2)-beta;
    1. LysM domain (1)
  8. Urease, gamma-subunit (1)
    alpha(3)-beta(2); antiparallel hairpin
    1. Urease, gamma-subunit (1)
  9. IL8-like (2)
    beta(3)-alpha
    1. Interleukin 8-like chemokines (1) pic
      form dimers with different dimerisation modes
    2. Chromo domain-like (2)
  10. DNA-binding domain (1)
    beta(3)-alpha; 2 layers: alpha/beta
    1. DNA-binding domain (3)
  11. Penicillin-binding protein 2x (pbp-2x), c-terminal domain (1)
    alpha1-beta3; 2 layers: alpha/beta; order 132
    1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain (1)
      duplication: consists of 2 subdomains of this fold
  12. Ribosomal proteins L23 and L15e (1)
    beta-(alpha)-beta-alpha-beta(2); 3 layers: alpha/beta/alpha; antiparallel beta-sheet: order 1243
    1. Ribosomal proteins L23 and L15e (2)
  13. HIT-like (1)
    alpha-beta3-alpha-beta2; 3 layers: alpha/beta/alpha
    1. HIT-like (2)
  14. Ribosomal protein S5 domain 2-like (1)
    core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
    1. Ribosomal protein S5 domain 2-like (5)
  15. beta-Grasp (ubiquitin-like) (9)
    core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
    1. Ubiquitin-like (5)
    2. CAD domain (1)
      possibly related to the ubiquitin-like superfamily
    3. MoaD/ThiS (2)
      possible link between the ubiquitin-like and 2Fe-2S ferredoxin-like superfamilies
    4. 2Fe-2S ferredoxin-like (2) pic
    5. Staphylokinase/streptokinase (1)
    6. Superantigen toxins, C-terminal domain (1)
    7. Immunoglobulin-binding domains (1) pic
    8. Translation initiation factor IF3, N-terminal domain (1)
    9. Glutamine synthetase, N-terminal domain (1) pic
  16. FAD-linked reductases, C-terminal domain (1)
    alpha+beta sandwich
    1. FAD-linked reductases, C-terminal domain (6) pic
      N-terminal domain is beta/beta/alpha common fold
  17. Cystatin-like (5)
    Core: alpha-beta(4); helix packs against coiled antiparallel beta-sheet
    1. Cystatin/monellin (2) pic
      has a additional strand at the N-terminus
    2. Copper amine oxidase, domains 1 and 2 (1)
    3. Disulfide bond isomerase, DsbC, N-terminal domain (1)
    4. NTF2-like (4)
      has a beta-alpha(2)-beta insertion after the main helix
    5. Uracil-DNA glycosylase inhibitor protein (1)
      has an additional strand at the C-terminus and a helix inserted after the first strand
  18. Transcriptional coactivator PC4 C-terminal domain (1)
    beta(4)-alpha; forms dimers by swapping helices
    1. Transcriptional coactivator PC4 C-terminal domain (1)
  19. MHC antigen-recognition domain (1)
    dimeric
    1. MHC antigen-recognition domain (1) pic
  20. Ubiquitin conjugating enzyme (1)
    alpha-beta(4)-alpha(3); core: meander beta-sheet plus one helix 2
    1. Ubiquitin conjugating enzyme (1)
  21. Diaminopimelate epimerase (1)
    mixed beta-sheet folds into a barrel (n=8, S=14) around the central helix
    1. Diaminopimelate epimerase (1)
      duplication: consists of two similar domain swapped with C-terminal strands
  22. Fluorescent proteins (1)
    beta-sheet folds into a barrel (n=11, S=14) around the central helix
    1. Fluorescent proteins (1)
  23. Transcriptional factor tubby, C-terminal domain (1)
    beta-sheet folds into a barrel (n=12, S=12) around the central helix
    1. Transcriptional factor tubby, C-terminal domain (1)
  24. Pilin (1)
    contains very long N-terminal helix, which end is packed against beta-sheet
    1. Pilin (1)
  25. Acidic mitochondrial matrix protein p32 (1)
    core: beta(7)-alpha(2); N- and C-terminal extensions form a coiled coil subdomain
    1. Acidic mitochondrial matrix protein p32 (1)
  26. FKBP-like (3)
    core: beta(2)-alpha-beta(2); antiparallel beta-sheet
    1. FKBP-like (2)
    2. Colicin E3 immunity protein (1)
    3. Chitinase insertion domain (1)
  27. Ribosomal protein S16 (1)
    beta(4)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet, order: 51234
    1. Ribosomal protein S16 (1)
  28. Ribosomal protein S19 (1)
    alpha-beta-X-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 123
    1. Ribosomal protein S19 (1)
  29. Ribosomal protein L31e (1)
    beta-alpha-beta-(aplha)-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 1342
    1. Ribosomal protein L31e (1)
  30. Allophycocyanin linker chain (domain) (1)
    beta(2)-alpha-beta; 2 layers: alpha/beta
    1. Allophycocyanin linker chain (domain) (1)
  31. Cdc48 domain 2-like (1)
    beta-alpha-beta(3); 2 layers: alpha/beta
    1. Cdc48 domain 2-like (1)
  32. Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (1)
    beta-alpha-beta(3); 2 layers: alpha/beta
    1. Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (3)
  33. Bacterial protein-export protein SecB (1)
    beta(4)-alpha(2); two layers: alpha/beta; antiparallel sheet: order 1432
    1. Bacterial protein-export protein SecB (1)
  34. DNA-binding domain of Mlu1-box binding protein MBP1 (1)
    beta(4)-alpha(2)-beta(2)-alpha; antiparallel sheet: order 123465
    1. DNA-binding domain of Mlu1-box binding protein MBP1 (1)
      has some topological similarity to the "winged helix" DNA-binding domain, to B1 and B5 domains of PheRS-beta (1PYS CH B) and to methyl-CpG-binding domain
  35. Heme-binding protein A (HasA) (1)
    beta-alpha-beta(6)-alpha(2); antiparallel sheet: order 165432
    1. Heme-binding protein A (HasA) (1)
  36. Chalcone isomerase (1)
    beta(3)-alpha(2)-beta-alpha(2)-beta3; 2 layers alpha/beta; antiparallel sheet: order 1234567
    1. Chalcone isomerase (1)
  37. CBS-domain (1)
    core: beta-alpha-beta(4); 2 layers: alpha/beta
    1. CBS-domain (1)
  38. Thioesterase/thiol ester dehydrase-isomerase (1)
    core: beta-alpha-beta(4); 2 layers: alpha/beta
    1. Thioesterase/thiol ester dehydrase-isomerase (3)
  39. Dynein light chain 8 (DLC8) (1)
    core: beta-alpha(2)-beta-X-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 1342
    1. Dynein light chain 8 (DLC8) (1)
  40. CI-2 family of serine protease inhibitors (1)
    alpha+beta sandwich; loop across free side of beta-sheet
    1. CI-2 family of serine protease inhibitors (1) pic
  41. alpha/beta-Hammerhead (5)
    core: beta-BETA-alpha-beta-BETA-beta-alpha; contains a beta-hammerhead motif similar to that in barrel-sandwich hybrids
    1. CO dehydrogenase molybdoprotein N-domain-like (1)
    2. Quinolinic acid phosphoribosyltransferase, N-terminal domain (1)
    3. Pyrimidine nucleoside phosphorylase C-terminal domain (1)
    4. Ribosomal protein L10e (1)
    5. Molybdopterin synthase subunit MoaE (1)
  42. POZ domain (1)
    core: beta(2)-alpha(2)-beta(2)-alpha(2); 2 layers a/b; mixed sheet: 2143
    1. POZ domain (2)
  43. Elongation factor Ts (EF-Ts), dimerisation domain (1)
    beta(2)-alpha(n)-beta; 2 layers a/b; antiparallel sheet: 123
    1. Elongation factor Ts (EF-Ts), dimerisation domain (1)
  44. Fe,Mn superoxide dismutase (SOD), C-terminal domain (1)
    alpha-beta(2)-alpha-beta-alpha(2); 3 strands of antiparallel sheet: 213
    1. Fe,Mn superoxide dismutase (SOD), C-terminal domain (1) pic
  45. Ribosomal protein L7/12, C-terminal domain (1)
    beta-alpha(2)-beta-alpha-beta; 2 layers, alpha/beta
    1. Ribosomal protein L7/12, C-terminal domain (1)
  46. Transcription-state regulator AbrB, the N-terminal DNA recognition domain (1)
    beta-alpha-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
    1. Transcription-state regulator AbrB, the N-terminal DNA recognition domain (1)
  47. Ribosomal protein L11, N-terminal domain (1)
    beta-alpha(2)-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
    1. Ribosomal protein L11, N-terminal domain (1)
  48. Anti-LPS factor/recA domain (2)
    alpha-beta(3)-alpha(2); 2 layers, alpha/beta
    1. RecA protein, C-terminal domain (1) pic
    2. Anti-lipopolysaccharide factor (1)
  49. Signal recognition particle alu RNA binding heterodimer, SRP9/14 (1)
    (beta)-alpha-beta(3)-alpha; 2 layers, alpha/beta
    1. Signal recognition particle alu RNA binding heterodimer, SRP9/14 (1)
  50. dsRBD-like (3)
    alpha-beta(3)-alpha; 2 layers: alpha/beta
    1. dsRNA-binding domain-like (2)
    2. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain (1)
    3. PI-Pfui intein middle domain (1)
  51. KH-domain (1)
    beta-alpha(2)-beta(2)-alpha; 2 layers: alpha/beta
    1. KH-domain (1)
  52. Alpha-lytic protease prodomain-like (3)
    core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta
    1. Alpha-lytic protease prodomain (1)
    2. GMP synthetase, C-terminal, dimerisation domain (1)
    3. Ribosomal protein S3 N-terminal domain-like (1)
      contains KH-motif
  53. Ribosomal protein S3 C-terminal domain (1)
    alpha(2)-beta(4); 2 layers: alpha/beta; antiparallel beta-sheet: order 2143
    1. Ribosomal protein S3 C-terminal domain (1)
  54. Enolase N-terminal domain-like (1)
    beta(3)-alpha(3); meander and up-and-down bundle
    1. Enolase N-terminal domain-like (1)
  55. Ribosomal protein L22 (1)
    beta-alpha(3)-beta(2); 2 layers: alpha/beta; related to the enolase/MLE N-domain fold by a circular permutation
    1. Ribosomal protein L22 (1)
  56. GroEL-like chaperone, intermediate domain (1)
    3-helical bundle packed against 3-stranded mixed beta-sheet
    1. GroEL-like chaperone, intermediate domain (2) pic
  57. DNA damage-inducible protein DinI (1)
    beta-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed sheet 213; crossing loops
    1. DNA damage-inducible protein DinI (1)
  58. Ferredoxin-like (36)
    alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
    1. 4Fe-4S ferredoxins (5)
    2. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain (1) pic
    3. Protease propeptides (2)
    4. Muconalactone isomerase (1)
    5. Prokaryotic signal transducing protein (1)
    6. Nucleoside diphosphate kinases (1)
    7. RNA-binding domain, RBD (2)
    8. Viral DNA-binding domain (1)
    9. RuBisCO, large subunit, small (N-terminal) domain (1)
      C-terminal domain is beta/alpha barrel
    10. Acylphosphatase (1) pic
    11. Elongation factor G (EF-G), domains III and V (1)
    12. eEF-1beta-like (1)
    13. Anticodon-binding domain of PheRS (1)
    14. Ribosomal protein S6 (1) pic
    15. Ribosomal protein S10 (1)
    16. Poly(A) polymerase, C-terminal domain (1)
    17. Metal-binding domain (1)
    18. Regulatory domain in the aminoacid metabolism (3)
    19. Carboxypeptidase G2, dimerisation domain (1)
    20. NAD-binding domain of HMG-CoA reductase (1)
    21. Molybdenum cofactor biosynthesis protein C, MoaC (1)
    22. TRADD, N-terminal domain (1)
    23. Probable ACP-binding domain of malonyl-CoA ACP transacylase (1) pic
    24. CheY-binding domain of CheA (1)
    25. Killer toxin KP6 alpha-subunit (1)
    26. Homoserine kinase, C-terminal domain (1)
      common fold is elaborated with additional secondary structures
    27. Translational regulator protein regA (1) pic
      common fold is elaborated with additional secondary structures
    28. Peptide methionine sulfoxide reductase (1)
      common fold is elaborated with additional secondary structures
    29. Adenylyl and guanylyl cyclase catalytic domain (1)
      common fold is elaborated with additional secondary structures
    30. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK (1)
      common fold is elaborated with additional secondary structures
    31. Methyl-coenzyme M reductase subunits (2)
      each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures
    32. FAD-linked oxidases, C-terminal domain (2)
      duplication: contains two subdomains of this fold
    33. Formylmethanofuran:tetrahydromethanopterin formyltransferase (1)
      duplication: contains two subdomains of this fold
    34. Formiminotransferase domain of formiminotransferase-cyclodeaminase. (1)
      duplication: contains two subdomains of this fold
    35. Pseudouridine synthase I (1)
      duplication: contains two subdomains of this fold
    36. Sulfite reductase, domains 1 and 3 (1)
      duplication: contains two subdomains of this fold
  59. Ribosomal protein L30p/L7e (1)
    core: beta-alpha-beta-alpha-beta; antiparallel beta-sheet: order 312; some similarity with the ferredoxin-like fold
    1. Ribosomal protein L30p/L7e (1)
  60. Probable bacterial effector-binding domain (1)
    duplication of beta-alpha-beta(2) motif: antiparallel beta sheet forms barrel (n=6, S=12)
    1. Probable bacterial effector-binding domain (2)
  61. tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase (1)
    duplication of beta-alpha-beta-alpha-beta motif: antiparallel beta sheet forms barrel (n=6, S=8) similar to the barrel of prokaryotic DNA topoisomerases I and III
    1. tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase (1)
  62. Pepsin inhibitor-3 (1)
    duplication of beta(3)-alpha(2) motif: meander beta sheets form barrel-like structure
    1. Pepsin inhibitor-3 (1)
  63. mRNA triphosphatase CET1 (1)
    duplication of beta-alpha-beta(3) motif: antiparallel beta sheet forms wide barrel (n=8, S=16) with a channel running through it
    1. mRNA triphosphatase CET1 (1)
  64. eIF1-like (1)
    beta(2)-alpha-beta(2)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet: order 51243
    1. eIF1-like (1)
  65. Hedgehog/DD-pepidase (1)
    alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
    1. Hedgehog/DD-pepidase (2)
      zinc-binding motif
  66. Alpha-L RNA-binding motif (1)
    alpha(2)-beta(2)-loop-beta; 2 layers: alpha/beta
    1. Alpha-L RNA-binding motif (3)
      common motif in otherwise different folds
  67. RRF/tRNA synthetase additional domain-like (3)
    core:alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
    1. Threonyl-tRNA synthetase (ThrRS), second 'additional' domain (1)
    2. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain (1)
    3. Ribosome recycling factor, RRF (1)
  68. IF3-like (2)
    beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest
    1. Translation initiation factor IF3 (1)
    2. EPT/RTPC-like (2)
  69. C-terminal domain of TolA (1)
    alpha-beta(2)-alpha-beta; 2 layers, alpha/beta; left-handed beta-alpha-beta unit
    1. C-terminal domain of TolA (1)
  70. Yest killer toxins (1)
    beta-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta; left-handed crossover connection
    1. Yest killer toxins (2)
  71. Cell division protein MinE topological specificity domain (1)
    dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
    1. Cell division protein MinE topological specificity domain (1)
  72. Cyanase C-terminal domain (1)
    intertwined dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
    1. Cyanase C-terminal domain (1)
  73. RuBisCO, small subunit (1)
    alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
    1. RuBisCO, small subunit (1)
  74. DCoH-like (4)
    beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
    1. Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) (1)
      has additional alpha helix at the N-terminus
    2. C-terminal domain of arginine repressor (1)
      forms trimers with three closely packed beta-sheets
    3. Dimerization subdomain of RNA polymerase alpha subunit N-terminal domain (1)
    4. Prokaryotic AspRS, insert domain (1)
  75. MutS N-terminal domain-like (2)
    beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
    1. tRNA splicing endonuclease EdnA, N-terminal domain (1)
    2. DNA repair protein MutS, domain I (1)
  76. GYF domain (1)
    beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
    1. GYF domain (1)
  77. Ribosomal protein L5 (1)
    beta-alpha-beta(2)-alpha-beta(3)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet: order 231654
    1. Ribosomal protein L5 (1)
  78. RPB5-like RNA polymerase subunit (1)
    core: beta-alpha-beta-alpha-beta(2); 2 layers, alpha/beta
    1. RPB5-like RNA polymerase subunit (2)
  79. Bacillus chorismate mutase-like (4)
    core: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
    1. YjgF-like (2)
      forms trimers with three closely packed beta-sheets
    2. Tubulin, C-terminal domain (1)
    3. L30e-like (2)
    4. Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain (1)
  80. Tautomerase/MIF (1)
    (beta-alpha-beta)2; 2 layers: alpha/beta; mixed beta-sheet
    forms trimers with three closely packed beta-sheets
    1. Tautomerase/MIF (3)
  81. Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (1)
    core: alpha-beta-alpha-beta(3); mixed sheet: 2134, strand 2 is parallel to strand 1
    1. Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (5) pic
      N-terminal domain is the classic Rossmann-fold
  82. N domain of copper amine oxidase-like (2)
    alpha-beta(5)-alpha; 2 layers: alpha/beta; meander antiparallel sheet
    1. Copper amine oxidase, domain N (1)
    2. Frataxin-like (1)
  83. Bactericidal permeability-increasing protein, BPI (1)
    beta-alpha-beta(5)-alpha-beta2; 2 layers: alpha/beta; antiparallel sheet
    1. Bactericidal permeability-increasing protein, BPI (1)
      duplication: consists of two clear structural repeats of this fold
  84. Subtilisin inhibitor (1)
    alpha+beta sandwich
    1. Subtilisin inhibitor (1)
  85. RNA bacteriophage capsid protein (1)
    6-standed beta-sheet followed with 2 helices; meander
    1. RNA bacteriophage capsid protein (1)
  86. Translation initiation factor eIF4e (1)
    beta(2)-alpha-beta(2)-alpha-beta(2)-alpha-beta-2; 2 layers: alpha/beta; antiparallel sheet: 21356478
    1. Translation initiation factor eIF4e (1)
  87. CO dehydrogenase flavoprotein C-domain-like (2)
    core: beta(3,4)-alpha(3); alpha+beta sandwich
    1. FAD/NAD-linked reductases, dimerisation (C-terminal) domain (1) pic
      both first two domains are of same beta/beta/alpha fold
    2. CO dehydrogenase flavoprotein C-terminal domain-like (1)
  88. SRF-like (1)
    alpha-beta(2)-alpha; dimer; 3 layers a/b/a; antiparallel beta-sheet
    1. SRF-like (1)
  89. The origin DNA-binding domain of SV40 T-antigen (1)
    alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers:a/b/a; antiparallel sheet 41325
    1. The origin DNA-binding domain of SV40 T-antigen (1)
  90. NADH oxidase/flavin reductase (1)
    core: (alpha-beta-alpha-beta)2; 3 layers a/b/a; antiparallel beta-sheet: 1243
    1. NADH oxidase/flavin reductase (1)
  91. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 (1)
    alpha-beta-alpha(2)-beta(3)-alpha; 3 layers a/b/a; antiparallel beta-sheet: 4123
    1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 (1)
  92. Zincin-like (2)
    contains mixed beta sheet with connection over free side of the sheet
    1. Metalloproteases ("zincins"), catalytic domain (11)
    2. Bacterial chitobiase, Domain 2 (1)
      contains similar fold but lacks its catalytic centre
  93. SH2-like (1)
    3 layers: a/b/a; antiparallel beta-sheet of 5 strands is flaked by two helices
    1. SH2 domain (1) pic
  94. Histidine-containing phosphocarrier proteins (HPr) (1)
    beta-alpha-beta(2)-alpha-beta-alpha; 2 layers: a/b; antiparallel sheet 1423
    1. Histidine-containing phosphocarrier proteins (HPr) (1) pic
  95. Homing endonuclease-like (2)
    alpha-beta(2)-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243
    1. Glucose permease domain IIB (1)
    2. Homing endonucleases (2)
  96. T-fold (1)
    beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234
    tunnel-shaped: its known members form wide oligomeric barrels different sizes
    1. Tetrahydrobiopterin biosynthesis enzymes-like (4)
      bind purine or pterin in topologically similar sites between subunits
  97. Cell cycle regulatory proteins (1)
    beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1243
    can form strand-exchange dimers
    1. Cell cycle regulatory proteins (1)
  98. beta-lactamase-inhibitor protein, BLIP (1)
    alpha(2)-beta(4); 2 layers: alpha/beta
    1. beta-lactamase-inhibitor protein, BLIP (1)
  99. Ribosomal protein L9 C-domain (1)
    alpha-beta-alpha(2)-beta(2); 2 layers: alpha/beta
    1. Ribosomal protein L9 C-domain (1)
  100. L9 N-domain-like (1)
    beta(2)-alpha-beta-alpha; 3 layers: alpha/beta/alpha
    1. L9 N-domain-like (2)
  101. Polynucleotide phosporylase/guanosine pentaphospate synthase (PNPase/GPSI), domains 2 and 5 (1)
    beta(2)-alpha-beta(2)-alpha; 3 layers: alpha/beta/alpha; antiparallel sheet: order 2134
    1. Polynucleotide phosporylase/guanosine pentaphospate synthase (PNPase/GPSI), domains 2 and 5 (1)
  102. Regulatory factor Nef (1)
    alpha(2)-beta(4)-alpha; 3 layers: alpha/beta/alpha
    1. Regulatory factor Nef (1)
  103. Mosquitocidal delta-endotoxin CytB (1)
    core: beta-alpha(2)-beta-alpha(2)-beta(4); 3 layers: a/b/a
    1. Mosquitocidal delta-endotoxin CytB (1)
  104. Class II aaRS and biotin synthetases (1)
    contains large mixed beta-sheet
    1. Class II aaRS and biotin synthetases (2) pic
  105. Clathrin adaptor appendage domain (1)
    beta-alpha-beta-alpha-beta(4)-alpha; 3 layers: a/b/a; bifurcated antiparallel beta-sheet
    1. Clathrin adaptor appendage domain (1)
  106. Sterol carrier protein 2 (SCP2) (1)
    alpha-beta(3)-(crossover)-beta-(alpha)-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 32145
    1. Sterol carrier protein 2 (SCP2) (1)
  107. Ran-binding protein mog1p (1)
    (beta-hairpin)-beta(3)-alpha-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet of 7 strands; order: 1237654
    1. Ran-binding protein mog1p (1)
  108. Acyl-CoA N-acyltransferases (Nat) (1)
    3 layers: a/b/a; contains mixed beta-sheet
    1. Acyl-CoA N-acyltransferases (Nat) (2)
  109. Actin depolymerizing proteins (1)
    3 layers: a/b/a; contains mixed beta-sheet
    1. Actin depolymerizing proteins (2)
  110. Profilin-like (3)
    core: 2 alpha-helices and 5-stranded sheet; 3 layers: alpha/beta/alpha
    1. Profilin (actin-binding protein) (1)
      alpha-beta(2)-alpha-beta(5)-alpha
    2. GAF domain (1)
      alpha(2)-beta(2)-alpha-beta(3)-alpha
    3. PYP-like sensor domain (3)
      alpha-beta(2)-alpha(2)-beta(3)
  111. PR-1-like (1)
    alpha-beta-alpha-beta-alpha(2)-beta(2); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
    1. PR-1-like (1)
  112. IIA domain of mannitol-specific and ntr phosphotransherase EII (1)
    beta-alpha(2)-beta(3)-alpha(3); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
    1. IIA domain of mannitol-specific and ntr phosphotransherase EII (1)
  113. Nucleoside triphosphate pyrophosphorylase (MutT) (1)
    beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet
    contains beta-grasp motif
    1. Nucleoside triphosphate pyrophosphorylase (MutT) (1)
  114. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (1)
    core: alpha-beta(2)-alpha-beta(2)-alpha-beta; 3 layers; mixed sheet: order 31425
    1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (1)
  115. Hypothetica protein YrdC (1)
    core: alpha-beta(2)-alpha-beta-alpha(2)-beta(2)-alpha-beta-alpha-beta(3); 3 layers; mixed twisted sheet of 9 strands
    1. Hypothetica protein YrdC (1)
  116. Hypothetica protein HI1434 (YbaK homologue) (1)
    core: alpha-beta-alpha-beta(2)-(alpha-beta)2-alpha-beta(2)-alpha-beta; 3 layers; bifurcated mixed sheet
    1. Hypothetica protein HI1434 (YbaK homologue) (1)
  117. Thymidylate synthase/dCMP hydroxymethylase (1)
    contains large mixed beta-sheet
    1. Thymidylate synthase/dCMP hydroxymethylase (1)
  118. Bacteriophage T7 lysozyme (Zn amidase) (1)
    contains mixed beta-sheet
    1. Bacteriophage T7 lysozyme (Zn amidase) (1)
  119. Streptomyces lysozyme (1)
    contains curved mixed beta-sheet; incomplete barrel
    1. Streptomyces lysozyme (1)
  120. Cytochrome b5 (1)
    small, heme-binding fold
    1. Cytochrome b5 (1)
  121. DNA topoisomerase I domain (1)
    beta(2)-alpha-beta-(alpha)-beta(2); left-handed crossover between strands 2 & 3
    1. DNA topoisomerase I domain (1)
  122. ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (1)
    8-stranded mixed beta-sheet; 2 layers: alpha/beta
    1. ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (3)
  123. Sporulation responce regulatory protein Spo0B (1)
    core: alpha-beta-alpha-beta(2)-(alpha)-beta(2)
    1. Sporulation responce regulatory protein Spo0B (1)
      Histidine kinase-like fold lacking the kinase ATP-binding site
  124. Ribonuclease Rh-like (1)
    alpha+beta fold
    1. Ribonuclease Rh-like (1)
  125. Ornithine decarboxylase C-terminal domain (1)
    complex alpha+beta motif
    1. Ornithine decarboxylase C-terminal domain (1)
  126. Pentein, beta/alpha-propeller (1)
    duplication: composed of 5 alpha-beta(2)-alpha-beta units arranged around pseudo fivefold axis
    1. Pentein (2)
  127. Creatinase/aminopeptidase (1)
    duplication: composed of two very similar alpha+beta folds
    1. Creatinase/aminopeptidase (1) pic
  128. Glutamine synthase/guanidino kinase catalytic domain (1)
    1. Glutamine synthase/guanidino kinase catalytic domain (2) pic
      duplication: common core consists of two beta-alpha-beta2-alpha repeats
  129. TBP-like (3)
    beta-alpha-beta(4)-alpha
    1. TATA-box binding protein-like (2)
    2. Phosphoglucomutase, C-terminal domain (1)
      contains a single copy of this fold and an extra beta-strand at the C-terminus
    3. Bet v1-like (3)
      contains a single copy of this fold with a alpha-beta2 insertion after the first helix; there is a cavity between the beta-sheet and the long C-terminal helix
  130. S-adenosylmethionine synthetase (1)
    duplication: consists of 3 similar intertwined domains
    structural repeat: beta-alpha-beta(2)-alpha-beta; two layers, alpha/beta
    1. S-adenosylmethionine synthetase (1) pic
  131. DNA clamp (1)
    contains two helices and two beta sheets
    duplication: fold has internal pseudo two-fold symmetry
    1. DNA clamp (2) pic
  132. Mitochondrial processing peptidase, MPP (1)
    beta(2)-alpha(2)-beta(2)-alpha(5)-beta; 2 layers: a/b; mixed sheet: order 15243: strands 2 to 5 are connected with a ferredoxin-like topology
    1. Mitochondrial processing peptidase, MPP (1)
      duplication: each subunit consists of two similar domains of this fold
  133. Molybdemum cofactor-binding domain (1)
    beta(2)-alpha-beta-alpha-beta; 2 layers: a/b; mixed sheet: order 1243: crossing loops
    1. Molybdemum cofactor-binding domain (1)
      duplication: consists of 4 structural repeats arranged in 2 lobes
      contains one left-hand beta-alpha-beta unit per lobe
  134. Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 (1)
    beta-alpha-beta-alpha-beta(3)-alpha(2,3); mixed sheet: order 12345; left-handed crossover connection bettween strands 2 and 3
    1. Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 (1)
      duplication: contains two domains of this fold
  135. The spindle assembly checkpoint protein mad2 (1)
    beta-alpha(2)-beta(2)-alpha-beta(3); mixed sheet: order 132465
    1. The spindle assembly checkpoint protein mad2 (1)
  136. Phospholipase D/nuclease (1)
    beta-alpha-beta-alpha-beta-alpha-beta(4)-alpha; mixed sheet: order 1765234
    1. Phospholipase D/nuclease (1)
  137. Monooxygenase (hydroxylase) regulatory protein (1)
    corner-like structure formed by two sheets and filled in with 2-3 helices
    1. Monooxygenase (hydroxylase) regulatory protein (1)
      duplication: consists of two beta-alpha-(beta)-beta(2) motifs; some topological similarity to the ferredoxin-like fold
  138. B3/B4 domain of PheRS, PheT (1)
    3 layers: beta/beta/alpha sandwich
    1. B3/B4 domain of PheRS, PheT (1)
  139. Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain (1)
    3 layers: alpha/beta/alpha; partial topological similarity to the ferredoxin-like fold
    1. Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain (1)
  140. Ribosomal protein S8 (1)
    consists of 2 different alpha+beta subdomains arranged in a 4-layer structure: b/a/b/a
    1. Ribosomal protein S8 (1)
  141. Ribosomal protein L6 (1)
    consists of two beta-sheets and one alpha-helix packed around single core
    1. Ribosomal protein L6 (1)
  142. ATP-grasp (2)
    Consists of two subdomains with different alpha+beta folds
    shares functional and structural similarities with the PIPK and protein kinase superfamilies
    1. Glutathione synthetase ATP-binding domain-like (6)
    2. DNA ligase/mRNA capping enzyme, catalytic domain (3)
      has a circularly permuted topology
  143. SAICAR synthase-like (1)
    consists of two alpha+beta subdomains
    1. SAICAR synthase-like (2)
      shares functional and structural similarities with the ATP-grasp fold and protein kinase superfamilies
  144. Protein kinase-like (PK-like) (1)
    consists of two alpha+beta domains, C-terminal domain is mostly alpha helical
    1. Protein kinase-like (PK-like) (4)
      shares functional and structural similarities with the ATP-grasp fold and PIPK
  145. FAD-binding domain (1)
    consists of two alpha+beta subdomains
    1. FAD-binding domain (3)
  146. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain (1)
    consists of two alpha+beta subdomains
    1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain (1)
  147. Methenyltetrahydromethanopterin cyclohydrolase (1)
    consists of two alpha+beta subdomains
    1. Methenyltetrahydromethanopterin cyclohydrolase (1)
  148. Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap) (1)
    consists of two alpha+beta domains; the N-terminal domain is array of helices and beta-hairpins; the C-terminal domain is an a/b sandwich with one left-handed beta-alpha(n)-beta unit
    1. Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap) (1)
  149. Nitrile hydratase alpha chain (1)
    4 layers a/b/b/a; inside is a sandwich of two 2-stranded beta-sheets
    1. Nitrile hydratase alpha chain (1)
      duplication: contains two structural repeats
  150. 4'-Phosphopantetheinyl transferase SFP (1)
    4 layers a/b/b/a; duplication of beta-alpha(3)-beta(2) motif
    1. 4'-Phosphopantetheinyl transferase SFP (1)
  151. DNase I-like (1)
    contains beta-sandwich; duplication of alpha+beta motif
    1. DNase I-like (1) pic
  152. Aldehyde ferredoxin oxidoreductase, N-terminal domain (1)
    contains sandwich; duplication of alpha+beta motif with single mixed sheet
    motif: beta(2)-alpha-beta(3)-alpha-beta; strand order 216345, strands 1 and 6 are parallel
    1. Aldehyde ferredoxin oxidoreductase, N-terminal domain (1)
  153. N-terminal nucleophile aminohydrolases (Ntn hydrolases) (1)
    4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
    1. N-terminal nucleophile aminohydrolases (Ntn hydrolases) (5)
      N-terminal residue provides two catalytic groups, nucleophile and proton donor
  154. L-aminopeptidase D-Ala-esterase/amidase (1)
    duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha
    1. L-aminopeptidase D-Ala-esterase/amidase (1)
      convergent similarity to the Ntn amidohydrolases
  155. Histidine decarboxylase (1)
    contains "silk" beta-sandwich flanked on both sides with alpha-helices
    1. Histidine decarboxylase (1)
      duplication: two structural repeats of 3 strands and 1 helix each
  156. S-adenosylmethionine decarboxylase (1)
    duplication of beta-alpha-beta(4)-alpha-beta-alpha-beta(2) motif; 4 layers a/b/b/a; antiparallel beta-sheets: order 23451687
    1. S-adenosylmethionine decarboxylase (1)
  157. Metallo-hydrolase/oxidoreductase (1)
    duplication of beta(4)-alpha-beta-alpha motif; 4 layers a/b/b/a; mixed beta-sheets
    1. Metallo-hydrolase/oxidoreductase (3)
  158. Protein serine/threonine phosphatase 2C (1)
    4 layers: alpha/beta/beta/alpha; antiparallel beta sheets
    1. Protein serine/threonine phosphatase 2C (1)
      contain binuclear metal (Mn) centre
  159. Metallo-dependent phosphatases (1)
    4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
    1. Metallo-dependent phosphatases (3)
  160. Nitrilase/N-carbamyl-D-aminoacid amidohydrolase (1)
    4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
    1. Nitrilase/N-carbamyl-D-aminoacid amidohydrolase (1)
      some topological similarities to the metallo-dependent phosphatases and DNase I-like nucleases
  161. Anthranilate synthase aminodeoxyisochorismate synthase/lyase subunit TrpE (1)
    duplication: contains four repeats of alpha-beta(2)-beta motif arranged in a 4 layer core structure: alpha/beta/beta/alpha; orthogonally packed beta-sheets
    1. Anthranilate synthase aminodeoxyisochorismate synthase/lyase subunit TrpE (1)
      the active site is formed by additional structures inserted into the core structure
  162. Lactate & malate dehydrogenases, C-terminal domain (1)
    unusual fold, defines family
    1. Lactate & malate dehydrogenases, C-terminal domain (1) pic
  163. DNA breaking-rejoining enzymes (1)
    core: alpha3-beta3-alpha4; one side of beta-sheet is exposed
    1. DNA breaking-rejoining enzymes (2)
  164. SMAD MH1 domain (1)
    consists of four alpha-helices and three beta-ribbons
    1. SMAD MH1 domain (1)
  165. Ribosome inactivating proteins (RIP) (1)
    contains mixed beta-sheet
    1. Ribosome inactivating proteins (RIP) (2) pic
  166. ADP-ribosylation (1)
    unusual fold
    1. ADP-ribosylation (2) pic
  167. Peptide deformylase (1)
    alpha-beta(5)-alpha; 3 layers: a/b/a; meander beta-sheet wraps around the C-terminal alpha-helix
    1. Peptide deformylase (1)
      nickel-dependent enzyme
  168. Succinate dehydrogenase/fumarate reductase catalytic domain (1)
    unusual fold
    1. Succinate dehydrogenase/fumarate reductase catalytic domain (1)
  169. C-type lectin-like (1)
    unusual fold
    1. C-type lectin-like (5)
  170. SRCR-like (2)
    unusual fold; disulphide-rich; core: beta-x-alpha-beta-loop-beta
    1. Scavenger receptor cysteine-rich (SRCR) domain (1)
    2. A heparin-binding domain (1)
  171. Fibrinogen C-terminal domains (1)
    unusual fold
    1. Fibrinogen C-terminal domains (1)
  172. gp120 core (1)
    unusual fold
    1. gp120 core (1)
  173. Methionine synthase (activation domain) (1)
    unusual fold
    1. Methionine synthase (activation domain) (1)
  174. Nitric oxide (NO) synthase oxygenase domain (1)
    unusual fold
    1. Nitric oxide (NO) synthase oxygenase domain (1)
  175. Penicillin-binding protein 2x (pbp-2x), N-terminal domain (1)
    unusual fold
    1. Penicillin-binding protein 2x (pbp-2x), N-terminal domain (1)
  176. Sulfite oxidase, middle catalytic domain (1)
    unusual fold; contains 3 layers of beta-sheet structure and a beta-grasp like motif
    1. Sulfite oxidase, middle catalytic domain (1)
  177. Fumarylacetoacetate hydrolase, FAH (1)
    unusual fold; contains 3 layers of beta-sheet structure and a SH3-like like motif
    1. Fumarylacetoacetate hydrolase, FAH (1)
  178. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains (1)
    unusual fold
    1. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains (1)
  179. Substrate-binding domain of HMG-CoA reductase (1)
    unusual fold
    1. Substrate-binding domain of HMG-CoA reductase (1)
  180. Conserved core of transcriptional regulatory protein vp16 (1)
    unusual fold
    1. Conserved core of transcriptional regulatory protein vp16 (1)
  181. Insert subdomain of RNA polymerase alpha subunit N-terminal domain (1)
    unusual fold; contains a left-handed beta-alpha-beta unit
    1. Insert subdomain of RNA polymerase alpha subunit N-terminal domain (1)
  182. Baseplate structural protein gp11 (1)
    unusual fold; trimer
    1. Baseplate structural protein gp11 (1)
  183. Major capsid protein gp5 (1)
    unusual fold
    1. Major capsid protein gp5 (1)
  184. Non-globular alpha_beta subunits of globular proteins (1)
    1. Non-globular alpha_beta subunits of globular proteins (1)
      this is not a true superfamily
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Generated from scop database 1.55 with scopm 1.095 on Mon Jul 9 18:35:50 2001
Copyright © 1994-2001 The scop authors / scop@mrc-lmb.cam.ac.uk