SMTL ID : 3oya.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and raltegravir at 2.65 resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 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.13: 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 SO4: SULFATE ION(Non-functional Binders)

SO4.2: 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 SO4.10: 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 SO4.14: 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 SO4.22: 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.165, T.166, S.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.166, A:T.166, A:S.167 GOL.4: 4 residues within 4Å: Chain A: P.138, S.139, Q.140, K.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.138, A:Q.140, A:Q.140 GOL.5: 4 residues within 4Å: Chain A: Q.63, Y.83 Chain E: P.280, F.281 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Q.63, A:Y.83, E:F.281 GOL.11: 7 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, I.275, D.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.270, B:D.276 GOL.15: 3 residues within 4Å: Chain E: S.165, T.166, S.167 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.166, E:S.167 GOL.16: 4 residues within 4Å: Chain E: P.138, S.139, Q.140, K.244 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:P.138, E:Q.140, E:Q.140 GOL.17: 4 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, Y.83 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:F.281, E:Q.63, E:Y.83, E:Y.83 GOL.23: 7 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, I.275, D.276 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.270, F:D.276

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

NH4.6: 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 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.119, E:D.119

6 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.8, RLT.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.6 MG.8: 6 residues within 4Å: Chain A: D.131, E.224, N.227 Chain D: A.17 Ligands: MG.7, RLT.9 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 MG.12: 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.6, H2O.6, H2O.7 MG.19: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.20, RLT.21 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.10, H2O.15 MG.20: 6 residues within 4Å: Chain E: D.131, E.224, N.227 Chain H: A.17 Ligands: MG.19, RLT.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.10 MG.24: 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.15, H2O.15, H2O.16

2 x RLT: N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide(Non-covalent)

RLT.9: 13 residues within 4Å: Chain A: D.131, D.188, Q.189, P.214, Y.215, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.7, MG.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.189, A:P.214, A:Y.215, A:P.217, A:E.224, A:E.224 Hydrogen bonds: A:Y.215 Water bridges: A:Y.132, A:Y.132, A:H.216, A:N.227 pi-Stacking: A:Y.215 RLT.21: 13 residues within 4Å: Chain E: D.131, D.188, Q.189, P.214, Y.215, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.19, MG.20 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Q.189, E:P.214, E:Y.215, E:P.217, E:E.224, E:E.224 Hydrogen bonds: E:Y.215 Water bridges: E:Y.132, E:H.216, E:N.227 pi-Stacking: E:Y.215

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

2010-10-20

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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