Lineage for Protein: Retroviral integrase, catalytic domain

  1. Root: SCOPe 2.06
  2. 2078559Class c: Alpha and beta proteins (a/b) [51349] (148 folds)
  3. 2122050Fold 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
  4. 2123751Superfamily c.55.3: Ribonuclease H-like [53098] (15 families) (S)
    consists of one domain of this fold
  5. 2124026Family c.55.3.2: Retroviral integrase, catalytic domain [53107] (2 protein domains)
  6. 2124027Protein Retroviral integrase, catalytic domain [53108] (4 species)

Species:

  1. 2124028Human immunodeficiency virus type 1 (new york-5 isolate) [TaxId:11698] [267758] (4 PDB entries)
    1. Domain for 4dmn:
    2. Domain for 4gvm:
    3. Domain for 4gw6:
    4. Domain for 4id1:
  2. 2124033Human immunodeficiency virus type 1 [TaxId:11676] [53110] (53 PDB entries)
    1. Domain for 1b92:
    2. Domain for 1b9d:
    3. Domain for 1b9f:
    4. Domain for 1bhl:
    5. Domains for 1bi4:
      1. 2124108Domain d1bi4a_: 1bi4 A: [33666]
      2. 2124109Domain d1bi4b_: 1bi4 B: [33667]
      3. 2124110Domain d1bi4c_: 1bi4 C: [33668]
    6. Domains for 1bis:
      1. 2124066Domain d1bisa_: 1bis A: [33650]
      2. 2124067Domain d1bisb_: 1bis B: [33651]
    7. Domains for 1biu:
      1. 2124098Domain d1biua_: 1biu A: [33663]
        protein/DNA complex; complexed with mg
      2. 2124099Domain d1biub_: 1biu B: [33664]
        protein/DNA complex; complexed with mg
      3. 2124100Domain d1biuc_: 1biu C: [33665]
        protein/DNA complex; complexed with mg
    8. Domains for 1biz:
      1. 2124069Domain d1biza_: 1biz A: [33652]
        complexed with cac
      2. 2124070Domain d1bizb_: 1biz B: [33653]
        complexed with cac
    9. Domains for 1bl3:
      1. 2124079Domain d1bl3a_: 1bl3 A: [33655]
        complexed with mg
      2. 2124080Domain d1bl3b_: 1bl3 B: [33656]
        complexed with mg
      3. 2124081Domain d1bl3c_: 1bl3 C: [33657]
        complexed with mg
    10. Domains for 1ex4:
      1. 2124112Domain d1ex4a2: 1ex4 A:56-222 [33670]
        Other proteins in same PDB: d1ex4a1, d1ex4b1
        complexed with cps
      2. 2124113Domain d1ex4b2: 1ex4 B:55-222 [33671]
        Other proteins in same PDB: d1ex4a1, d1ex4b1
        complexed with cps
    11. Domains for 1exq:
      1. 2124044Domain d1exqa_: 1exq A: [33646]
        complexed with cd, cl, so4
      2. 2124045Domain d1exqb_: 1exq B: [33647]
        complexed with cd, cl, so4
    12. Domain for 1hyv:
      • 2124046Domain d1hyva_: 1hyv A: [61424]
        protein/DNA complex; complexed with cl, so4, tta
    13. Domain for 1hyz:
      • 2124102Domain d1hyza_: 1hyz A: [61426]
        protein/DNA complex; complexed with cl, so4, tto
    14. Domain for 1itg:
    15. Domains for 1k6y:
      1. 2124103Domain d1k6ya2: 1k6y A:56-210 [68240]
        Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
        complexed with k, po4, zn
      2. 2124104Domain d1k6yb2: 1k6y B:56-212 [68242]
        Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
        complexed with k, po4, zn
      3. 2124105Domain d1k6yc2: 1k6y C:56-209 [68244]
        Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
        complexed with k, po4, zn
      4. 2124106Domain d1k6yd2: 1k6y D:56-211 [68246]
        Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
        complexed with k, po4, zn
    16. Domains for 1qs4:
      1. 2124086Domain d1qs4a_: 1qs4 A: [33658]
        protein/DNA complex; complexed with 100, mg
      2. 2124087Domain d1qs4b_: 1qs4 B: [33659]
        protein/DNA complex; complexed with 100, mg
      3. 2124088Domain d1qs4c_: 1qs4 C: [33660]
        protein/DNA complex; complexed with 100, mg
    17. Domains for 2b4j:
      1. 2124054Domain d2b4ja_: 2b4j A: [127833]
        Other proteins in same PDB: d2b4jc1, d2b4jc2, d2b4jd2, d2b4jd3
        automated match to d1bi4c_
        complexed with gol, po4
      2. 2124055Domain d2b4jb_: 2b4j B: [127834]
        Other proteins in same PDB: d2b4jc1, d2b4jc2, d2b4jd2, d2b4jd3
        automated match to d1bi4c_
        complexed with gol, po4
    18. Domain for 2itg:
    19. Domains for 3ao1:
      1. 2124056Domain d3ao1a_: 3ao1 A: [172279]
        automated match to d1bi4c_
        protein/DNA complex; complexed with bzx, cd, so4
      2. 2124057Domain d3ao1b_: 3ao1 B: [172280]
        automated match to d1bi4c_
        protein/DNA complex; complexed with bzx, cd, so4
    20. Domains for 3l3u:
      1. 2124034Domain d3l3ua_: 3l3u A: [236775]
        automated match to d3ao1a_
        complexed with so4
      2. 2124035Domain d3l3ub_: 3l3u B: [236773]
        automated match to d3ovnb_
        complexed with so4
    21. Domains for 3l3v:
      1. 2124090Domain d3l3va_: 3l3v A: [236772]
        automated match to d3ao1b_
        protein/DNA complex; complexed with cd, so4, suc
      2. 2124091Domain d3l3vb_: 3l3v B: [236774]
        automated match to d3ovnb_
        protein/DNA complex; complexed with cd, so4, suc
    22. Domains for 3ovn:
      1. 2124071Domain d3ovna_: 3ovn A: [183318]
        automated match to d1bi4c_
        protein/DNA complex; complexed with cd, mpv, so4, suc
      2. 2124072Domain d3ovnb_: 3ovn B: [183319]
        automated match to d1bi4c_
        protein/DNA complex; complexed with cd, mpv, so4, suc
    23. Domains for 3vq4:
      1. 2124062Domain d3vq4a_: 3vq4 A: [218019]
        automated match to d2itga_
        protein/DNA complex; complexed with 0nx, cd, so4
      2. 2124063Domain d3vq4b_: 3vq4 B: [218020]
        automated match to d2itga_
        protein/DNA complex; complexed with 0nx, cd, so4
    24. Domains for 3vq5:
      1. 2124038Domain d3vq5a_: 3vq5 A: [218021]
        automated match to d1bizb_
        protein/DNA complex; complexed with cd, cl, mmj, so4
      2. 2124039Domain d3vq5b_: 3vq5 B: [218022]
        automated match to d1bizb_
        protein/DNA complex; complexed with cd, cl, mmj, so4
    25. Domains for 3vq6:
      1. 2124052Domain d3vq6a_: 3vq6 A: [218023]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with bck, cd, so4
      2. 2124053Domain d3vq6b_: 3vq6 B: [218024]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with bck, cd, so4
    26. Domains for 3vq7:
      1. 2124036Domain d3vq7a_: 3vq7 A: [218025]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, snu, so4, suc
      2. 2124037Domain d3vq7b_: 3vq7 B: [218026]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, snu, so4, suc
    27. Domains for 3vq8:
      1. 2124042Domain d3vq8a_: 3vq8 A: [218027]
        automated match to d1bizb_
        protein/DNA complex; complexed with bcu, cd, cl, so4
      2. 2124043Domain d3vq8b_: 3vq8 B: [218028]
        automated match to d1bizb_
        protein/DNA complex; complexed with bcu, cd, cl, so4
    28. Domains for 3vq9:
      1. 2124049Domain d3vq9a_: 3vq9 A: [193266]
        automated match to d1bl3c_
        protein/DNA complex; complexed with fbb
      2. 2124050Domain d3vq9b_: 3vq9 B: [193267]
        automated match to d1bl3c_
        protein/DNA complex; complexed with fbb
      3. 2124051Domain d3vq9c_: 3vq9 C: [201255]
        automated match to d3vq9b_
        protein/DNA complex; complexed with fbb
    29. Domains for 3vqa:
      1. 2124064Domain d3vqaa_: 3vqa A: [218029]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with cd, mwp, so4, suc
      2. 2124065Domain d3vqab_: 3vqa B: [218030]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with cd, mwp, so4, suc
    30. Domains for 3vqb:
      1. 2124082Domain d3vqba_: 3vqb A: [218031]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, fbg, so4
      2. 2124083Domain d3vqbb_: 3vqb B: [218032]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, fbg, so4
    31. Domains for 3vqc:
      1. 2124096Domain d3vqca_: 3vqc A: [218033]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, mpk, so4
      2. 2124097Domain d3vqcb_: 3vqc B: [218034]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, mpk, so4
    32. Domains for 3vqd:
      1. 2124073Domain d3vqda_: 3vqd A: [218035]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, mok, so4
      2. 2124074Domain d3vqdb_: 3vqd B: [218036]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, mok, so4
    33. Domains for 3vqe:
      1. 2124040Domain d3vqea_: 3vqe A: [218037]
        automated match to d1bizb_
        protein/DNA complex; protein/RNA complex; complexed with cd, cl, fmq, so4
      2. 2124041Domain d3vqeb_: 3vqe B: [218038]
        automated match to d1bizb_
        protein/DNA complex; protein/RNA complex; complexed with cd, cl, fmq, so4
    34. Domains for 3vqp:
      1. 2124075Domain d3vqpa_: 3vqp A: [218039]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with cd, cl, dbj, so4
      2. 2124076Domain d3vqpb_: 3vqp B: [218040]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with cd, cl, dbj, so4
    35. Domains for 3vqq:
      1. 2124060Domain d3vqqa_: 3vqq A: [218041]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with bte, cd, so4, suc
      2. 2124061Domain d3vqqb_: 3vqq B: [218042]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with bte, cd, so4, suc
    36. Domain for 4lh4:
    37. Domain for 4lh5:
    38. Domains for 4nyf:
      1. 2124084Domain d4nyfa_: 4nyf A: [263234]
        automated match to d3vq9c_
        complexed with 4bi, cd
      2. 2124085Domain d4nyfb_: 4nyf B: [257202]
        automated match to d3vq9c_
        complexed with 4bi, cd
    39. Domain for 4o0j:
    40. Domain for 4o55:
    41. Domain for 4o5b:
    42. Domain for 4ojr:
    43. Domains for 4ovl:
      1. 2124058Domain d4ovla_: 4ovl A: [237439]
        automated match to d4ah9a_
        complexed with 1td, acy, edo, gol, so4
      2. 2124059Domain d4ovlb_: 4ovl B: [237438]
        automated match to d4ah9a_
        complexed with 1td, acy, edo, gol, so4
    44. Domain for 4tsx:
    45. Domains for 5eu7:
      1. 2280022Domain d5eu7a_: 5eu7 A: [323323]
        Other proteins in same PDB: d5eu7c1, d5eu7c2, d5eu7d1, d5eu7d2
        automated match to d1bisa_
      2. 2280061Domain d5eu7b_: 5eu7 B: [323362]
        Other proteins in same PDB: d5eu7c1, d5eu7c2, d5eu7d1, d5eu7d2
        automated match to d1bisa_
    46. Domain for 5hrn:
      • 2283885Domain d5hrna_: 5hrn A: [327186]
        automated match to d3vq9c_
        protein/DNA complex; complexed with 65p, cac, edo, so4; mutant
    47. Domain for 5hrp:
      • 2283833Domain d5hrpa_: 5hrp A: [327134]
        automated match to d3vq9c_
        protein/DNA complex; complexed with 65p, cac, edo, so4; mutant
    48. Domain for 5hrr:
      • 2283894Domain d5hrra_: 5hrr A: [327195]
        automated match to d3vq9c_
        protein/DNA complex; complexed with 65p, cac, edo, so4; mutant
    49. Domain for 5hrs:
      • 2283847Domain d5hrsa_: 5hrs A: [327148]
        automated match to d3vq9c_
        protein/DNA complex; complexed with 65p, cac, edo, so4; mutant
    50. Domains for 5jl4:
      1. 2296480Domain d5jl4a_: 5jl4 A: [339781]
        automated match to d3vq9c_
        complexed with so4; mutant
      2. 2296481Domain d5jl4b_: 5jl4 B: [339782]
        automated match to d3vq9c_
        complexed with so4; mutant
    51. Domain for 5kgw:
    52. Domain for 5krs:
    53. Domain for 5krt:
  3. 2124114Rous sarcoma virus RSV [TaxId:11886] [53109] (23 PDB entries)
    1. Domain for 1a5v:
    2. Domain for 1a5w:
    3. Domain for 1a5x:
    4. Domain for 1asu:
    5. Domain for 1asv:
    6. Domain for 1asw:
    7. Domains for 1c0m:
      1. 2124137Domain d1c0ma2: 1c0m A:49-216 [33640]
        Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
      2. 2124138Domain d1c0mb2: 1c0m B:54-216 [33641]
        Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
      3. 2124139Domain d1c0mc2: 1c0m C:49-216 [33642]
        Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
      4. 2124140Domain d1c0md2: 1c0m D:54-216 [33643]
        Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
    8. Domains for 1c1a:
      1. 2124141Domain d1c1aa2: 1c1a A:52-216 [33644]
        Other proteins in same PDB: d1c1aa1, d1c1ab1
      2. 2124142Domain d1c1ab2: 1c1a B:55-216 [33645]
        Other proteins in same PDB: d1c1aa1, d1c1ab1
    9. Domain for 1cxq:
    10. Domain for 1cxu:
    11. Domain for 1cz9:
    12. Domain for 1czb:
    13. Domain for 1vsd:
    14. Domain for 1vse:
    15. Domain for 1vsf:
    16. Domain for 1vsh:
    17. Domain for 1vsi:
    18. Domain for 1vsj:
    19. Domain for 1vsk:
    20. Domain for 1vsl:
    21. Domain for 1vsm:
    22. Domains for 3o4n:
      1. 2124123Domain d3o4na_: 3o4n A: [182791]
        automated match to d1asua_
        complexed with mes, zn
      2. 2124124Domain d3o4nb_: 3o4n B: [182792]
        automated match to d1asua_
        complexed with mes, zn
    23. Domain for 3o4q:
  4. 2124143Simian immunodeficiency virus [TaxId:11723] [53111] (1 PDB entry)

More info for Protein Retroviral integrase, catalytic domain from c.55.3.2: Retroviral integrase, catalytic domain

Timeline for Protein Retroviral integrase, catalytic domain from c.55.3.2: Retroviral integrase, catalytic domain: