Lineage for Protein: Retroviral integrase, catalytic domain

  1. Root: SCOPe 2.08
  2. 2826024Class c: Alpha and beta proteins (a/b) [51349] (148 folds)
  3. 2883383Fold 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. 2885833Superfamily c.55.3: Ribonuclease H-like [53098] (18 families) (S)
    consists of one domain of this fold
  5. 2886113Family c.55.3.2: Retroviral integrase, catalytic domain [53107] (2 proteins)
    Pfam PF00665
  6. 2886114Protein Retroviral integrase, catalytic domain [53108] (5 species)

Species:

  1. 2886115Human 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. 2886120Human immunodeficiency virus type 1 [TaxId:11676] [53110] (73 PDB entries)
    1. Domain for 1b92:
    2. Domain for 1b9d:
    3. Domain for 1b9f:
    4. Domain for 1bhl:
    5. Domains for 1bi4:
      1. 2886218Domain d1bi4a_: 1bi4 A: [33666]
      2. 2886219Domain d1bi4b_: 1bi4 B: [33667]
      3. 2886220Domain d1bi4c_: 1bi4 C: [33668]
    6. Domains for 1bis:
      1. 2886144Domain d1bisa_: 1bis A: [33650]
      2. 2886145Domain d1bisb_: 1bis B: [33651]
    7. Domains for 1biu:
      1. 2886191Domain d1biua_: 1biu A: [33663]
        protein/DNA complex; complexed with mg
      2. 2886192Domain d1biub_: 1biu B: [33664]
        protein/DNA complex; complexed with mg
      3. 2886193Domain d1biuc_: 1biu C: [33665]
        protein/DNA complex; complexed with mg
    8. Domains for 1biz:
      1. 2886147Domain d1biza_: 1biz A: [33652]
        complexed with cac
      2. 2886148Domain d1bizb_: 1biz B: [33653]
        complexed with cac
    9. Domains for 1bl3:
      1. 2886163Domain d1bl3a_: 1bl3 A: [33655]
        complexed with mg
      2. 2886164Domain d1bl3b_: 1bl3 B: [33656]
        complexed with mg
      3. 2886165Domain d1bl3c_: 1bl3 C: [33657]
        complexed with mg
    10. Domains for 1ex4:
      1. 2886233Domain d1ex4a2: 1ex4 A:56-222 [33670]
        Other proteins in same PDB: d1ex4a1, d1ex4b1
        complexed with cps
      2. 2886234Domain d1ex4b2: 1ex4 B:55-222 [33671]
        Other proteins in same PDB: d1ex4a1, d1ex4b1
        complexed with cps
    11. Domains for 1exq:
      1. 2886142Domain d1exqa_: 1exq A: [33646]
        complexed with cd, cl, so4
      2. 2886143Domain d1exqb_: 1exq B: [33647]
        complexed with cd, cl, so4
    12. Domain for 1hyv:
      • 2886159Domain d1hyva_: 1hyv A: [61424]
        protein/DNA complex; complexed with cl, so4, tta
    13. Domain for 1hyz:
      • 2886225Domain d1hyza_: 1hyz A: [61426]
        protein/DNA complex; complexed with cl, so4, tto
    14. Domain for 1itg:
    15. Domains for 1k6y:
      1. 2886203Domain d1k6ya2: 1k6y A:56-210 [68240]
        Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
        complexed with k, po4, zn
      2. 2886204Domain d1k6yb2: 1k6y B:56-212 [68242]
        Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
        complexed with k, po4, zn
      3. 2886205Domain d1k6yc2: 1k6y C:56-209 [68244]
        Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
        complexed with k, po4, zn
      4. 2886206Domain 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. 2886212Domain d1qs4a_: 1qs4 A: [33658]
        protein/DNA complex; complexed with 100, mg
      2. 2886213Domain d1qs4b_: 1qs4 B: [33659]
        protein/DNA complex; complexed with 100, mg
      3. 2886214Domain d1qs4c_: 1qs4 C: [33660]
        protein/DNA complex; complexed with 100, mg
    17. Domains for 2b4j:
      1. 2886201Domain d2b4ja_: 2b4j A: [127833]
        Other proteins in same PDB: d2b4jc1, d2b4jc2, d2b4jd2, d2b4jd3
        automated match to d1bi4c_
        complexed with gol, po4
      2. 2886202Domain 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. 2886136Domain d3ao1a_: 3ao1 A: [172279]
        automated match to d1bi4c_
        protein/DNA complex; complexed with bzx, cd, so4
      2. 2886137Domain d3ao1b_: 3ao1 B: [172280]
        automated match to d1bi4c_
        protein/DNA complex; complexed with bzx, cd, so4
    20. Domains for 3l3u:
      1. 2886121Domain d3l3ua_: 3l3u A: [236775]
        automated match to d3ao1a_
        complexed with so4
      2. 2886122Domain d3l3ub_: 3l3u B: [236773]
        automated match to d3ovnb_
        complexed with so4
    21. Domains for 3l3v:
      1. 2886167Domain d3l3va_: 3l3v A: [236772]
        automated match to d3ao1b_
        protein/DNA complex; complexed with cd, so4
      2. 2886168Domain d3l3vb_: 3l3v B: [236774]
        automated match to d3ovnb_
        protein/DNA complex; complexed with cd, so4
    22. Domains for 3ovn:
      1. 2886173Domain d3ovna_: 3ovn A: [183318]
        automated match to d1bi4c_
        protein/DNA complex; complexed with cd, mpv, so4
      2. 2886174Domain d3ovnb_: 3ovn B: [183319]
        automated match to d1bi4c_
        protein/DNA complex; complexed with cd, mpv, so4
    23. Domains for 3vq4:
      1. 2886140Domain d3vq4a_: 3vq4 A: [218019]
        automated match to d2itga_
        protein/DNA complex; complexed with 0nx, cd, so4
      2. 2886141Domain d3vq4b_: 3vq4 B: [218020]
        automated match to d2itga_
        protein/DNA complex; complexed with 0nx, cd, so4
    24. Domains for 3vq5:
      1. 2886123Domain d3vq5a_: 3vq5 A: [218021]
        automated match to d1bizb_
        protein/DNA complex; complexed with cd, cl, mmj, so4
      2. 2886124Domain d3vq5b_: 3vq5 B: [218022]
        automated match to d1bizb_
        protein/DNA complex; complexed with cd, cl, mmj, so4
    25. Domains for 3vq6:
      1. 2886134Domain d3vq6a_: 3vq6 A: [218023]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with bck, cd, so4
      2. 2886135Domain d3vq6b_: 3vq6 B: [218024]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with bck, cd, so4
    26. Domains for 3vq7:
      1. 2886129Domain d3vq7a_: 3vq7 A: [218025]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, snu, so4
      2. 2886130Domain d3vq7b_: 3vq7 B: [218026]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, snu, so4
    27. Domains for 3vq8:
      1. 2886127Domain d3vq8a_: 3vq8 A: [218027]
        automated match to d1bizb_
        protein/DNA complex; complexed with bcu, cd, cl, so4
      2. 2886128Domain d3vq8b_: 3vq8 B: [218028]
        automated match to d1bizb_
        protein/DNA complex; complexed with bcu, cd, cl, so4
    28. Domains for 3vq9:
      1. 2886131Domain d3vq9a_: 3vq9 A: [193266]
        automated match to d1bl3c_
        protein/DNA complex; complexed with fbb
      2. 2886132Domain d3vq9b_: 3vq9 B: [193267]
        automated match to d1bl3c_
        protein/DNA complex; complexed with fbb
      3. 2886133Domain d3vq9c_: 3vq9 C: [201255]
        automated match to d3vq9b_
        protein/DNA complex; complexed with fbb
    29. Domains for 3vqa:
      1. 2886160Domain d3vqaa_: 3vqa A: [218029]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with cd, mwp, so4
      2. 2886161Domain d3vqab_: 3vqa B: [218030]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with cd, mwp, so4
    30. Domains for 3vqb:
      1. 2886169Domain d3vqba_: 3vqb A: [218031]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, fbg, so4
      2. 2886170Domain d3vqbb_: 3vqb B: [218032]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, fbg, so4
    31. Domains for 3vqc:
      1. 2886189Domain d3vqca_: 3vqc A: [218033]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, mpk, so4
      2. 2886190Domain d3vqcb_: 3vqc B: [218034]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, mpk, so4
    32. Domains for 3vqd:
      1. 2886150Domain d3vqda_: 3vqd A: [218035]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, mok, so4
      2. 2886151Domain d3vqdb_: 3vqd B: [218036]
        automated match to d2itga_
        protein/DNA complex; complexed with cd, mok, so4
    33. Domains for 3vqe:
      1. 2886125Domain d3vqea_: 3vqe A: [218037]
        automated match to d1bizb_
        protein/DNA complex; protein/RNA complex; complexed with cd, cl, fmq, so4
      2. 2886126Domain 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. 2886152Domain d3vqpa_: 3vqp A: [218039]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with cd, cl, dbj, so4
      2. 2886153Domain 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. 2886178Domain d3vqqa_: 3vqq A: [218041]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with bte, cd, so4
      2. 2886179Domain d3vqqb_: 3vqq B: [218042]
        automated match to d2itga_
        protein/DNA complex; protein/RNA complex; complexed with bte, cd, so4
    36. Domain for 4lh4:
    37. Domain for 4lh5:
    38. Domains for 4nyf:
      1. 2886171Domain d4nyfa_: 4nyf A: [263234]
        automated match to d3vq9c_
        complexed with 4bi, cd
      2. 2886172Domain 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. 2886138Domain d4ovla_: 4ovl A: [237439]
        automated match to d4ah9a_
        complexed with 1td, acy, edo, gol, so4
      2. 2886139Domain d4ovlb_: 4ovl B: [237438]
        automated match to d4ah9a_
        complexed with 1td, acy, edo, gol, so4
    44. Domain for 4tsx:
    45. Domains for 5eu7:
      1. 2886235Domain d5eu7a_: 5eu7 A: [323323]
        Other proteins in same PDB: d5eu7c1, d5eu7c2, d5eu7d1, d5eu7d2, d5eu7e_, d5eu7f_
        automated match to d1bisa_
      2. 2886236Domain d5eu7b_: 5eu7 B: [323362]
        Other proteins in same PDB: d5eu7c1, d5eu7c2, d5eu7d1, d5eu7d2, d5eu7e_, d5eu7f_
        automated match to d1bisa_
    46. Domain for 5hrn:
      • 2886177Domain d5hrna_: 5hrn A: [327186]
        automated match to d3vq9c_
        protein/DNA complex; complexed with 65p, cac, edo, so4; mutant
    47. Domain for 5hrp:
      • 2886180Domain d5hrpa_: 5hrp A: [327134]
        automated match to d3vq9c_
        protein/DNA complex; complexed with 65p, cac, edo, so4; mutant
    48. Domain for 5hrr:
      • 2886184Domain d5hrra_: 5hrr A: [327195]
        automated match to d3vq9c_
        protein/DNA complex; complexed with 65p, cac, edo, so4; mutant
    49. Domain for 5hrs:
      • 2886182Domain d5hrsa_: 5hrs A: [327148]
        automated match to d3vq9c_
        protein/DNA complex; complexed with 65p, cac, edo, so4; mutant
    50. Domains for 5jl4:
      1. 2886175Domain d5jl4a_: 5jl4 A: [339781]
        automated match to d3vq9c_
        complexed with so4; mutant
      2. 2886176Domain d5jl4b_: 5jl4 B: [339782]
        automated match to d3vq9c_
        complexed with so4; mutant
    51. Domain for 5kgw:
    52. Domain for 5krs:
    53. Domain for 5krt:
    54. Domain for 5oi3:
    55. Domain for 5oi8:
    56. Domain for 5oia:
    57. Domain for 6eb1:
    58. Domain for 6eb2:
    59. Domain for 6ex9:
    60. Domain for 6jcf:
    61. Domain for 6jcg:
    62. Domain for 6lmi:
    63. Domain for 6lmq:
    64. Domain for 6ncj:
    65. Domain for 6nuj:
    66. Domains for 6vka:
      1. 2886155Domain d6vkaa_: 6vka A: [400650]
        automated match to d3vq9c_
        complexed with iod, qzv, so4
      2. 2886156Domain d6vkab_: 6vka B: [400671]
        automated match to d3vq9c_
        complexed with iod, qzv, so4
    67. Domains for 6vlh:
      1. 2886187Domain d6vlha_: 6vlh A: [400654]
        automated match to d3vq9c_
        complexed with iod, r2a, so4
      2. 2886188Domain d6vlhb_: 6vlh B: [400677]
        automated match to d3vq9c_
        complexed with iod, r2a, so4
    68. Domains for 6vrg:
      1. 2886196Domain d6vrga2: 6vrg A:56-211 [392787]
        Other proteins in same PDB: d6vrga1, d6vrgb1, d6vrgc1, d6vrgd1
        automated match to d1k6yb2
        complexed with k, po4, zn
      2. 2886197Domain d6vrgb2: 6vrg B:56-210 [392796]
        Other proteins in same PDB: d6vrga1, d6vrgb1, d6vrgc1, d6vrgd1
        automated match to d1k6ya2
        complexed with k, po4, zn
      3. 2886198Domain d6vrgc2: 6vrg C:56-210 [392808]
        Other proteins in same PDB: d6vrga1, d6vrgb1, d6vrgc1, d6vrgd1
        automated match to d1k6ya2
        complexed with k, po4, zn
      4. 2886199Domain d6vrgd2: 6vrg D:56-209 [392820]
        Other proteins in same PDB: d6vrga1, d6vrgb1, d6vrgc1, d6vrgd1
        automated match to d1k6ya2
        complexed with k, po4, zn
    69. Domain for 6vx2:
    70. Domain for 6w0u:
    71. Domain for 6wc8:
    72. Domain for 6we7:
    73. Domain for 7d83:
  3. 2886237Human spumaretrovirus [TaxID:11963] [419615] (6 PDB entries)
    1. Domain for 3l2q:
    2. Domain for 3l2s:
    3. Domain for 3l2u:
    4. Domain for 3s3n:
    5. Domain for 3s3o:
    6. Domains for 4ztj:
      1. 2886243Domain d4ztja2: 4ztj A:107-315 [414549]
        Other proteins in same PDB: d4ztja1, d4ztja3
        automated match to d3l2qa1
        protein/DNA complex; complexed with 4rt, gol, mg, so4, zn
      2. 2886244Domain d4ztjb_: 4ztj B: [414551]
        Other proteins in same PDB: d4ztja1, d4ztja3
        automated match to d3l2qa1
        protein/DNA complex; complexed with 4rt, gol, mg, so4, zn
  4. 2886245Rous 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. 2886268Domain d1c0ma2: 1c0m A:49-216 [33640]
        Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
      2. 2886269Domain d1c0mb2: 1c0m B:54-216 [33641]
        Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
      3. 2886270Domain d1c0mc2: 1c0m C:49-216 [33642]
        Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
      4. 2886271Domain d1c0md2: 1c0m D:54-216 [33643]
        Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
    8. Domains for 1c1a:
      1. 2886272Domain d1c1aa2: 1c1a A:52-216 [33644]
        Other proteins in same PDB: d1c1aa1, d1c1ab1
      2. 2886273Domain 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. 2886254Domain d3o4na_: 3o4n A: [182791]
        automated match to d1asua_
        complexed with mes, zn
      2. 2886255Domain d3o4nb_: 3o4n B: [182792]
        automated match to d1asua_
        complexed with mes, zn
    23. Domain for 3o4q:
  5. 2886274Simian immunodeficiency virus [TaxId:11723] [53111] (3 PDB entries)
    1. Domains for 1c6v:
      1. 2886279Domain d1c6va_: 1c6v A: [33672]
        Other proteins in same PDB: d1c6vx_
        mutant
      2. 2886280Domain d1c6vb_: 1c6v B: [33673]
        Other proteins in same PDB: d1c6vx_
        mutant
      3. 2886281Domain d1c6vc_: 1c6v C: [33674]
        Other proteins in same PDB: d1c6vx_
        mutant
      4. 2886282Domain d1c6vd_: 1c6v D: [33675]
        Other proteins in same PDB: d1c6vx_
        mutant
    2. Domains for 6rwm:
      1. 2886275Domain d6rwmd1: 6rwm D:57-222 [380198]
        Other proteins in same PDB: d6rwmc1, d6rwmc2, d6rwmd2, d6rwme1, d6rwme2, d6rwmf1, d6rwmk1, d6rwmk2, d6rwml2, d6rwmm1, d6rwmm2, d6rwmn1
        automated match to d1ex4b2
        protein/DNA complex; complexed with cl, klq, mg, zn
      2. 2886276Domain d6rwml1: 6rwm L:57-222 [380238]
        Other proteins in same PDB: d6rwmc1, d6rwmc2, d6rwmd2, d6rwme1, d6rwme2, d6rwmf1, d6rwmk1, d6rwmk2, d6rwml2, d6rwmm1, d6rwmm2, d6rwmn1
        automated match to d1ex4b2
        protein/DNA complex; complexed with cl, klq, mg, zn
    3. Domains for 6rwn:
      1. 2886277Domain d6rwnd1: 6rwn D:57-222 [380196]
        Other proteins in same PDB: d6rwnc1, d6rwnc2, d6rwnd2, d6rwne1, d6rwne2, d6rwnf1, d6rwnk1, d6rwnk2, d6rwnl2, d6rwnm1, d6rwnm2, d6rwnn1
        automated match to d1ex4b2
        protein/DNA complex; complexed with cl, dlu, mg, zn
      2. 2886278Domain d6rwnl1: 6rwn L:57-222 [380220]
        Other proteins in same PDB: d6rwnc1, d6rwnc2, d6rwnd2, d6rwne1, d6rwne2, d6rwnf1, d6rwnk1, d6rwnk2, d6rwnl2, d6rwnm1, d6rwnm2, d6rwnn1
        automated match to d1ex4b2
        protein/DNA complex; complexed with cl, dlu, mg, zn

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: