SCOPe 2.03: Protein: Retroviral integrase, catalytic domain

Lineage for Protein: Retroviral integrase, catalytic domain

Root: SCOPe 2.03
Class c: Alpha and beta proteins (a/b) [51349] (147 folds)
Fold 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
Superfamily c.55.3: Ribonuclease H-like [53098] (15 families)
consists of one domain of this fold
Family c.55.3.2: Retroviral integrase, catalytic domain [53107] (2 proteins)
Protein Retroviral integrase, catalytic domain [53108] (3 species)

Species:

Human immunodeficiency virus type 1 [TaxId:11676] [53110] (37 PDB entries)
1. Domain for 1b92:
  - Domain d1b92a_: 1b92 A: [33654]
    complexed with cac, so4
2. Domain for 1b9d:
  - Domain d1b9da_: 1b9d A: [33649]
    complexed with cac, so4
3. Domain for 1b9f:
  - Domain d1b9fa_: 1b9f A: [33648]
    complexed with cac, so4
4. Domain for 1bhl:
  - Domain d1bhla_: 1bhl A: [33662]
5. Domains for 1bi4:
  1. Domain d1bi4a_: 1bi4 A: [33666]
  2. Domain d1bi4b_: 1bi4 B: [33667]
  3. Domain d1bi4c_: 1bi4 C: [33668]
6. Domains for 1bis:
  1. Domain d1bisa_: 1bis A: [33650]
  2. Domain d1bisb_: 1bis B: [33651]
7. Domains for 1biu:
  1. Domain d1biua_: 1biu A: [33663]
    protein/DNA complex; complexed with mg
  2. Domain d1biub_: 1biu B: [33664]
    protein/DNA complex; complexed with mg
  3. Domain d1biuc_: 1biu C: [33665]
    protein/DNA complex; complexed with mg
8. Domains for 1biz:
  1. Domain d1biza_: 1biz A: [33652]
    complexed with cac
  2. Domain d1bizb_: 1biz B: [33653]
    complexed with cac
9. Domains for 1bl3:
  1. Domain d1bl3a_: 1bl3 A: [33655]
    complexed with mg
  2. Domain d1bl3b_: 1bl3 B: [33656]
    complexed with mg
  3. Domain d1bl3c_: 1bl3 C: [33657]
    complexed with mg
10. Domains for 1ex4:
  1. Domain d1ex4a2: 1ex4 A:56-222 [33670]
    Other proteins in same PDB: d1ex4a1, d1ex4b1
    complexed with cps
  2. Domain d1ex4b2: 1ex4 B:55-222 [33671]
    Other proteins in same PDB: d1ex4a1, d1ex4b1
    complexed with cps
11. Domains for 1exq:
  1. Domain d1exqa_: 1exq A: [33646]
    complexed with cd, cl, so4
  2. Domain d1exqb_: 1exq B: [33647]
    complexed with cd, cl, so4
12. Domain for 1hyv:
  - Domain d1hyva_: 1hyv A: [61424]
    protein/DNA complex; complexed with cl, so4, tta
13. Domain for 1hyz:
  - Domain d1hyza_: 1hyz A: [61426]
    protein/DNA complex; complexed with cl, so4, tto
14. Domain for 1itg:
  - Domain d1itga_: 1itg A: [33661]
    complexed with cac
15. Domains for 1k6y:
  1. Domain d1k6ya2: 1k6y A:56-210 [68240]
    Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
    complexed with k, po4, zn
  2. Domain d1k6yb2: 1k6y B:56-212 [68242]
    Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
    complexed with k, po4, zn
  3. Domain d1k6yc2: 1k6y C:56-209 [68244]
    Other proteins in same PDB: d1k6ya1, d1k6yb1, d1k6yc1, d1k6yd1
    complexed with k, po4, zn
  4. Domain 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. Domain d1qs4a_: 1qs4 A: [33658]
    protein/DNA complex; complexed with 100, mg
  2. Domain d1qs4b_: 1qs4 B: [33659]
    protein/DNA complex; complexed with 100, mg
  3. Domain d1qs4c_: 1qs4 C: [33660]
    protein/DNA complex; complexed with 100, mg
17. Domains for 2b4j:
  1. Domain d2b4ja_: 2b4j A: [127833]
    Other proteins in same PDB: d2b4jc1, d2b4jd_
    automated match to d1bi4c_
    complexed with gol, po4
  2. Domain d2b4jb_: 2b4j B: [127834]
    Other proteins in same PDB: d2b4jc1, d2b4jd_
    automated match to d1bi4c_
    complexed with gol, po4
18. Domain for 2itg:
  - Domain d2itga_: 2itg A: [33669]
19. Domains for 3ao1:
  1. Domain d3ao1a_: 3ao1 A: [172279]
    automated match to d1bi4c_
    protein/DNA complex; complexed with bzx, cd, so4
  2. Domain d3ao1b_: 3ao1 B: [172280]
    automated match to d1bi4c_
    protein/DNA complex; complexed with bzx, cd, so4
20. Domains for 3l3u:
  1. Domain d3l3ua_: 3l3u A: [236775]
    automated match to d3ao1a_
    complexed with so4
  2. Domain d3l3ub_: 3l3u B: [236773]
    automated match to d3ovnb_
    complexed with so4
21. Domains for 3l3v:
  1. Domain d3l3va_: 3l3v A: [236772]
    automated match to d3ao1b_
    protein/DNA complex; complexed with cd, so4, suc
  2. Domain d3l3vb_: 3l3v B: [236774]
    automated match to d3ovnb_
    protein/DNA complex; complexed with cd, so4, suc
22. Domains for 3ovn:
  1. Domain d3ovna_: 3ovn A: [183318]
    automated match to d1bi4c_
    protein/DNA complex; complexed with cd, mpv, so4, suc
  2. Domain d3ovnb_: 3ovn B: [183319]
    automated match to d1bi4c_
    protein/DNA complex; complexed with cd, mpv, so4, suc
23. Domains for 3vq4:
  1. Domain d3vq4a_: 3vq4 A: [218019]
    automated match to d2itga_
    protein/DNA complex; complexed with 0nx, cd, so4
  2. Domain d3vq4b_: 3vq4 B: [218020]
    automated match to d2itga_
    protein/DNA complex; complexed with 0nx, cd, so4
24. Domains for 3vq5:
  1. Domain d3vq5a_: 3vq5 A: [218021]
    automated match to d1bizb_
    protein/DNA complex; complexed with cd, cl, mmj, so4
  2. Domain d3vq5b_: 3vq5 B: [218022]
    automated match to d1bizb_
    protein/DNA complex; complexed with cd, cl, mmj, so4
25. Domains for 3vq6:
  1. Domain d3vq6a_: 3vq6 A: [218023]
    automated match to d2itga_
    protein/DNA complex; protein/RNA complex; complexed with bck, cd, so4
  2. Domain d3vq6b_: 3vq6 B: [218024]
    automated match to d2itga_
    protein/DNA complex; protein/RNA complex; complexed with bck, cd, so4
26. Domains for 3vq7:
  1. Domain d3vq7a_: 3vq7 A: [218025]
    automated match to d2itga_
    protein/DNA complex; complexed with cd, snu, so4, suc
  2. Domain d3vq7b_: 3vq7 B: [218026]
    automated match to d2itga_
    protein/DNA complex; complexed with cd, snu, so4, suc
27. Domains for 3vq8:
  1. Domain d3vq8a_: 3vq8 A: [218027]
    automated match to d1bizb_
    protein/DNA complex; complexed with bcu, cd, cl, so4
  2. Domain d3vq8b_: 3vq8 B: [218028]
    automated match to d1bizb_
    protein/DNA complex; complexed with bcu, cd, cl, so4
28. Domains for 3vq9:
  1. Domain d3vq9a_: 3vq9 A: [193266]
    automated match to d1bl3c_
    protein/DNA complex; complexed with fbb
  2. Domain d3vq9b_: 3vq9 B: [193267]
    automated match to d1bl3c_
    protein/DNA complex; complexed with fbb
  3. Domain d3vq9c_: 3vq9 C: [201255]
    automated match to d3vq9b_
    protein/DNA complex; complexed with fbb
29. Domains for 3vqa:
  1. Domain d3vqaa_: 3vqa A: [218029]
    automated match to d2itga_
    protein/DNA complex; protein/RNA complex; complexed with cd, mwp, so4, suc
  2. Domain 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. Domain d3vqba_: 3vqb A: [218031]
    automated match to d2itga_
    protein/DNA complex; complexed with cd, fbg, so4
  2. Domain d3vqbb_: 3vqb B: [218032]
    automated match to d2itga_
    protein/DNA complex; complexed with cd, fbg, so4
31. Domains for 3vqc:
  1. Domain d3vqca_: 3vqc A: [218033]
    automated match to d2itga_
    protein/DNA complex; complexed with cd, mpk, so4
  2. Domain d3vqcb_: 3vqc B: [218034]
    automated match to d2itga_
    protein/DNA complex; complexed with cd, mpk, so4
32. Domains for 3vqd:
  1. Domain d3vqda_: 3vqd A: [218035]
    automated match to d2itga_
    protein/DNA complex; complexed with cd, mok, so4
  2. Domain d3vqdb_: 3vqd B: [218036]
    automated match to d2itga_
    protein/DNA complex; complexed with cd, mok, so4
33. Domains for 3vqe:
  1. Domain d3vqea_: 3vqe A: [218037]
    automated match to d1bizb_
    protein/DNA complex; protein/RNA complex; complexed with cd, cl, fmq, so4
  2. Domain 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. Domain d3vqpa_: 3vqp A: [218039]
    automated match to d2itga_
    protein/DNA complex; protein/RNA complex; complexed with cd, cl, dbj, so4
  2. Domain 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. Domain d3vqqa_: 3vqq A: [218041]
    automated match to d2itga_
    protein/DNA complex; protein/RNA complex; complexed with bte, cd, so4, suc
  2. Domain d3vqqb_: 3vqq B: [218042]
    automated match to d2itga_
    protein/DNA complex; protein/RNA complex; complexed with bte, cd, so4, suc
36. Domain for 4lh4:
  - Domain d4lh4a_: 4lh4 A: [230119]
    automated match to d3vq9c_
    complexed with mg
37. Domain for 4lh5:
  - Domain d4lh5a_: 4lh5 A: [235372]
    automated match to d4lh4a_
    complexed with lf0, mg
Rous sarcoma virus RSV [TaxId:11886] [53109] (23 PDB entries)
1. Domain for 1a5v:
  - Domain d1a5va_: 1a5v A: [33629]
    complexed with mn, y3
2. Domain for 1a5w:
  - Domain d1a5wa_: 1a5w A: [33632]
    complexed with y3
3. Domain for 1a5x:
  - Domain d1a5xa_: 1a5x A: [33630]
    complexed with y3
4. Domain for 1asu:
  - Domain d1asua_: 1asu A: [33626]
    complexed with epe
5. Domain for 1asv:
  - Domain d1asva_: 1asv A: [33634]
6. Domain for 1asw:
  - Domain d1aswa_: 1asw A: [33627]
    complexed with epe, ipa
7. Domains for 1c0m:
  1. Domain d1c0ma2: 1c0m A:49-216 [33640]
    Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
  2. Domain d1c0mb2: 1c0m B:54-216 [33641]
    Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
  3. Domain d1c0mc2: 1c0m C:49-216 [33642]
    Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
  4. Domain d1c0md2: 1c0m D:54-216 [33643]
    Other proteins in same PDB: d1c0ma1, d1c0mb1, d1c0mc1, d1c0md1
8. Domains for 1c1a:
  1. Domain d1c1aa2: 1c1a A:52-216 [33644]
    Other proteins in same PDB: d1c1aa1, d1c1ab1
  2. Domain d1c1ab2: 1c1a B:55-216 [33645]
    Other proteins in same PDB: d1c1aa1, d1c1ab1
9. Domain for 1cxq:
  - Domain d1cxqa_: 1cxq A: [33621]
    complexed with epe, gol
10. Domain for 1cxu:
  - Domain d1cxua_: 1cxu A: [33624]
    complexed with cit, gol
11. Domain for 1cz9:
  - Domain d1cz9a_: 1cz9 A: [33623]
    complexed with cit, so4
12. Domain for 1czb:
  - Domain d1czba_: 1czb A: [33622]
    complexed with epe
13. Domain for 1vsd:
  - Domain d1vsda_: 1vsd A: [33625]
    complexed with epe, mg
14. Domain for 1vse:
  - Domain d1vsea_: 1vse A: [33631]
    complexed with epe
15. Domain for 1vsf:
  - Domain d1vsfa_: 1vsf A: [33628]
    complexed with epe, mn
16. Domain for 1vsh:
  - Domain d1vsha_: 1vsh A: [33633]
    complexed with epe, zn
17. Domain for 1vsi:
  - Domain d1vsia_: 1vsi A: [33638]
    complexed with ca, epe
18. Domain for 1vsj:
  - Domain d1vsja_: 1vsj A: [33636]
    complexed with cd, epe
19. Domain for 1vsk:
  - Domain d1vska_: 1vsk A: [33639]
    mutant
20. Domain for 1vsl:
  - Domain d1vsla_: 1vsl A: [33637]
    complexed with zn; mutant
21. Domain for 1vsm:
  - Domain d1vsma_: 1vsm A: [33635]
22. Domains for 3o4n:
  1. Domain d3o4na_: 3o4n A: [182791]
    automated match to d1asua_
    complexed with mes, zn
  2. Domain d3o4nb_: 3o4n B: [182792]
    automated match to d1asua_
    complexed with mes, zn
23. Domain for 3o4q:
  - Domain d3o4qa_: 3o4q A: [182793]
    automated match to d1asua_
    complexed with flc
Simian immunodeficiency virus [TaxId:11723] [53111] (1 PDB entry)
- Domains for 1c6v:
  1. Domain d1c6va_: 1c6v A: [33672]
    Other proteins in same PDB: d1c6vx_
    mutant
  2. Domain d1c6vb_: 1c6v B: [33673]
    Other proteins in same PDB: d1c6vx_
    mutant
  3. Domain d1c6vc_: 1c6v C: [33674]
    Other proteins in same PDB: d1c6vx_
    mutant
  4. Domain d1c6vd_: 1c6v D: [33675]
    Other proteins in same PDB: d1c6vx_
    mutant

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:

Protein Retroviral integrase, catalytic domain from c.55.3.2: Retroviral integrase, catalytic domain first appeared (with stable ids) in SCOP 1.55
Protein Retroviral integrase, catalytic domain from c.55.3.2: Retroviral integrase, catalytic domain appears in SCOPe 2.02
Protein Retroviral integrase, catalytic domain from c.55.3.2: Retroviral integrase, catalytic domain appears in SCOPe 2.04
Protein Retroviral integrase, catalytic domain from c.55.3.2: Retroviral integrase, catalytic domain appears in the current release, SCOPe 2.08