- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.53 Å
- Oligo State
- homo-tetramer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)
MN.2: 5 residues within 4Å:- Chain A: D.131, D.188
- Chain D: A.18
- Ligands: MN.3, MES.12
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:D.131, A:D.188, H2O.1, H2O.5, H2O.10
MN.3: 6 residues within 4Å:- Chain A: D.131, E.224, N.227
- Chain D: A.17, A.18
- Ligands: MN.2
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.131, A:E.224, A:E.224, H2O.1
MN.13: 2 residues within 4Å:- Chain B: D.131, D.188
5 PLIP interactions:2 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:D.131, B:D.188, H2O.7, H2O.7, H2O.8
MN.21: 5 residues within 4Å:- Chain E: D.131, D.188
- Chain H: A.18
- Ligands: MN.22, MES.31
5 PLIP interactions:2 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:D.131, E:D.188, H2O.11, H2O.16, H2O.20
MN.22: 6 residues within 4Å:- Chain E: D.131, E.224, N.227
- Chain H: A.17, A.18
- Ligands: MN.21
4 PLIP interactions:3 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:D.131, E:E.224, E:E.224, H2O.11
MN.32: 2 residues within 4Å:- Chain F: D.131, D.188
5 PLIP interactions:2 interactions with chain F, 3 Ligand-Water interactions- Metal complexes: F:D.131, F:D.188, H2O.17, H2O.17, H2O.19
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 2 residues within 4Å:- Chain A: H.341, K.342
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.342
- Salt bridges: A:H.341, A:K.342
SO4.5: 4 residues within 4Å:- Chain A: T.161, K.162, A.163, A.168
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.162, A:A.163
- Water bridges: A:S.165
SO4.10: 5 residues within 4Å:- Chain A: R.117, Y.306, P.308
- Chain C: C.6
- Ligands: GOL.17
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.306
- Water bridges: A:R.117
- Salt bridges: A:R.117
SO4.14: 5 residues within 4Å:- Chain B: K.222, R.225, S.261, P.262, V.263
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.261, B:V.263
- Salt bridges: B:K.222, B:R.225
SO4.23: 2 residues within 4Å:- Chain E: H.341, K.342
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.342
- Salt bridges: E:H.341, E:K.342
SO4.24: 4 residues within 4Å:- Chain E: T.161, K.162, A.163, A.168
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.162, E:A.163
- Water bridges: E:S.165
SO4.29: 5 residues within 4Å:- Chain E: R.117, Y.306, P.308
- Chain G: C.6
- Ligands: GOL.36
2 PLIP interactions:2 interactions with chain E- Water bridges: E:R.117
- Salt bridges: E:R.117
SO4.33: 5 residues within 4Å:- Chain F: K.222, R.225, S.261, P.262, V.263
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:S.261, F:V.263
- Salt bridges: F:K.222, F:R.225
- 18 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 4 residues within 4Å:- Chain A: P.138, S.139, Q.140, K.244
Ligand excluded by PLIPGOL.7: 5 residues within 4Å:- Chain A: Q.63, L.82, Y.83
- Chain E: P.280, F.281
Ligand excluded by PLIPGOL.8: 3 residues within 4Å:- Chain A: P.118, D.119
- Chain C: T.3
Ligand excluded by PLIPGOL.9: 3 residues within 4Å:- Chain A: S.165, T.166, S.167
Ligand excluded by PLIPGOL.11: 4 residues within 4Å:- Chain A: Q.189, T.194, F.211
- Chain C: A.1
Ligand excluded by PLIPGOL.16: 7 residues within 4Å:- Chain A: L.295, Q.299
- Chain B: Y.266, Q.270, G.274, I.275, D.276
Ligand excluded by PLIPGOL.17: 7 residues within 4Å:- Chain A: V.263, Y.306
- Chain C: C.6, A.7, T.8
- Chain D: C.11
- Ligands: SO4.10
Ligand excluded by PLIPGOL.18: 4 residues within 4Å:- Chain D: A.15, C.16, A.17, A.18
Ligand excluded by PLIPGOL.19: 6 residues within 4Å:- Chain D: A.7, T.8
- Chain E: L.76, W.84, M.88, R.89
Ligand excluded by PLIPGOL.25: 4 residues within 4Å:- Chain E: P.138, S.139, Q.140, K.244
Ligand excluded by PLIPGOL.26: 5 residues within 4Å:- Chain A: P.280, F.281
- Chain E: Q.63, L.82, Y.83
Ligand excluded by PLIPGOL.27: 3 residues within 4Å:- Chain E: P.118, D.119
- Chain G: T.3
Ligand excluded by PLIPGOL.28: 3 residues within 4Å:- Chain E: S.165, T.166, S.167
Ligand excluded by PLIPGOL.30: 4 residues within 4Å:- Chain E: Q.189, T.194, F.211
- Chain G: A.1
Ligand excluded by PLIPGOL.35: 7 residues within 4Å:- Chain E: L.295, Q.299
- Chain F: Y.266, Q.270, G.274, I.275, D.276
Ligand excluded by PLIPGOL.36: 7 residues within 4Å:- Chain E: V.263, Y.306
- Chain G: C.6, A.7, T.8
- Chain H: C.11
- Ligands: SO4.29
Ligand excluded by PLIPGOL.37: 4 residues within 4Å:- Chain H: A.15, C.16, A.17, A.18
Ligand excluded by PLIPGOL.38: 6 residues within 4Å:- Chain A: L.76, W.84, M.88, R.89
- Chain H: A.7, T.8
Ligand excluded by PLIP- 2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.12: 7 residues within 4Å:- Chain A: Y.132, Y.144, P.164, G.190, A.191
- Chain D: A.18
- Ligands: MN.2
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.191
- Water bridges: A:A.192, A:A.192
MES.31: 7 residues within 4Å:- Chain E: Y.132, Y.144, P.164, G.190, A.191
- Chain H: A.18
- Ligands: MN.21
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:A.191
- Water bridges: E:A.192, E:A.192
- 2 x HEZ: HEXANE-1,6-DIOL(Non-covalent)
HEZ.15: 8 residues within 4Å:- Chain A: S.178, I.179
- Chain B: W.157, L.158, Y.159, Y.246, P.250, Q.253
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Y.159
HEZ.34: 8 residues within 4Å:- Chain E: S.178, I.179
- Chain F: W.157, L.158, Y.159, Y.246, P.250, Q.253
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:Y.159
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hare, S. et al., 3'-Processing and strand transfer catalysed by retroviral integrase in crystallo. Embo J. (2012)
- Release Date
- 2012-05-23
- Peptides
- Pro-Pol polyprotein: ABEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.53 Å
- Oligo State
- homo-tetramer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)
- 8 x SO4: SULFATE ION(Non-functional Binders)
- 18 x GOL: GLYCEROL(Non-functional Binders)
- 2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 2 x HEZ: HEXANE-1,6-DIOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hare, S. et al., 3'-Processing and strand transfer catalysed by retroviral integrase in crystallo. Embo J. (2012)
- Release Date
- 2012-05-23
- Peptides
- Pro-Pol polyprotein: ABEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
B