SMTL ID : 3oyi.1

Crystal structure of the PFV S217Q mutant intasome in complex with manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-tetramer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.11: 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

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.131, Y.132, E.224, N.227 Chain D: A.17 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.1, H2O.5 MN.9: 2 residues within 4Å: Chain B: D.131, D.188 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.131, B:D.188, H2O.5, H2O.5 MN.12: 5 residues within 4Å: Chain E: D.131, Y.132, E.224, N.227 Chain H: A.17 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.8, H2O.13 MN.19: 2 residues within 4Å: Chain F: D.131, D.188 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.131, F:D.188, H2O.13, H2O.13

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

SO4.3: 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 SO4.10: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.263 Salt bridges: B:K.222, B:R.225 SO4.13: 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 SO4.20: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.263 Salt bridges: F:K.222, F:R.225

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: S.165, T.166, S.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.166, A:T.166, A:S.167, A:S.167, A:S.167 GOL.5: 3 residues within 4Å: Chain A: S.139, Q.140, K.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.140, A:Q.140 GOL.6: 6 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, I.275, D.276 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.276, A:Q.299 GOL.7: 5 residues within 4Å: Chain A: Q.63, L.82, Y.83 Chain E: P.280, F.281 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Q.63, E:F.281 GOL.14: 3 residues within 4Å: Chain E: S.165, T.166, S.167 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.166, E:S.167, E:S.167, E:S.167 GOL.15: 3 residues within 4Å: Chain E: S.139, Q.140, K.244 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.140, E:Q.140 GOL.16: 6 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, I.275, D.276 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.299, F:D.276, F:D.276 GOL.17: 5 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, L.82, Y.83 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Q.63, E:Y.83, A:F.281

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.8: 2 residues within 4Å: Chain A: P.118, D.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.119 NH4.18: 2 residues within 4Å: Chain E: P.118, D.119 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hare, S. et al., Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-11-17

Peptides

PFV integrase: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

PFV integrase

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