SMTL ID : 4e7h.1

PFV intasome prior to 3'-processing, Apo form (UI-Apo)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-tetramer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: H.341, K.342, H.360 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.342 Salt bridges: A:H.341, A:K.342, A:H.360 SO4.4: 5 residues within 4Å: Chain A: N.174, T.177, S.178, R.205 Chain B: P.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.174, A:T.177 Salt bridges: A:R.205 SO4.5: 5 residues within 4Å: Chain A: T.161, K.162, A.163, A.168, K.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.162, A:A.163 Water bridges: A:S.165, A:S.165 SO4.8: 5 residues within 4Å: Chain A: R.117, Y.306, P.308 Chain C: C.6 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.306 Water bridges: A:R.117 Salt bridges: A:R.117 SO4.11: 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 SO4.17: 3 residues within 4Å: Chain E: H.341, K.342, H.360 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.342 Salt bridges: E:H.341, E:K.342, E:H.360 SO4.20: 5 residues within 4Å: Chain E: N.174, T.177, S.178, R.205 Chain F: P.250 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.174, E:T.177 Salt bridges: E:R.205 SO4.21: 5 residues within 4Å: Chain E: T.161, K.162, A.163, A.168, K.171 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.162, E:A.163 Water bridges: E:S.165, E:S.165 SO4.24: 5 residues within 4Å: Chain E: R.117, Y.306, P.308 Chain G: C.6 Ligands: GOL.30 2 PLIP interactions: 2 interactions with chain E Water bridges: E:R.117 Salt bridges: E:R.117 SO4.27: 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.2: 3 residues within 4Å: Chain A: S.165, T.166, S.167 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: Q.63, L.82, Y.83 Chain E: P.280, F.281 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: P.118, D.119 Chain C: T.3 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: Q.189, T.194, F.211 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, D.276 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain B: I.130, H.186, S.187, D.188, N.227 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain A: V.263, Y.306 Chain C: C.6, A.7, T.8 Chain D: C.11, A.12 Ligands: SO4.8 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain D: C.16, A.17, A.18 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain D: A.7, T.8 Chain E: L.76, A.80, W.84, M.88, R.89 Ligands: HEZ.25 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain E: S.165, T.166, S.167 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, L.82, Y.83 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain E: P.118, D.119 Chain G: T.3 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain E: Q.189, T.194, F.211 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, D.276 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain F: I.130, H.186, S.187, D.188, N.227 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain E: V.263, Y.306 Chain G: C.6, A.7, T.8 Chain H: C.11, A.12 Ligands: SO4.24 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain H: C.16, A.17, A.18 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain A: L.76, A.80, W.84, M.88, R.89 Chain H: A.7, T.8 Ligands: HEZ.9 Ligand excluded by PLIP

2 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.9: 8 residues within 4Å: Chain A: E.73, L.77, A.80, R.89 Chain E: K.265 Chain H: T.8, T.9 Ligands: GOL.32 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:L.77, E:K.265 HEZ.25: 8 residues within 4Å: Chain A: K.265 Chain D: T.8, T.9 Chain E: E.73, L.77, A.80, R.89 Ligands: GOL.16 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:L.77, A:K.265 Hydrogen bonds: E:E.73

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain A: H.65, H.69, C.99, C.102 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.65, A:H.69, A:C.99, A:C.102 ZN.26: 4 residues within 4Å: Chain E: H.65, H.69, C.99, C.102 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.65, E:H.69, E:C.99, E:C.102

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
A

B
B

E
A

F
B

Pro-Pol polyprotein

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