SMTL ID : 4bdy.1

PFV intasome with inhibitor XZ-89

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 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

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

SO4.2: 3 residues within 4Å: Chain A: H.341, K.342, H.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.342 Salt bridges: A:H.341, A:H.360 SO4.9: 4 residues within 4Å: Chain A: D.188, Q.189, P.214, Y.215 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.189, A:Y.215 Water bridges: A:T.213, A:H.216 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 SO4.14: 3 residues within 4Å: Chain E: H.341, K.342, H.360 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.342 Salt bridges: E:H.341, E:H.360 SO4.21: 4 residues within 4Å: Chain E: D.188, Q.189, P.214, Y.215 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.189, E:Y.215 Water bridges: E:D.188, E:T.213, E:H.216 SO4.23: 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

10 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.138, A:Q.140 GOL.5: 4 residues within 4Å: Chain A: Q.63, Y.83 Chain E: P.280, F.281 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:F.281, A:Q.63 GOL.10: 3 residues within 4Å: Chain A: P.118, D.119 Chain C: T.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.119, A:D.119 GOL.12: 6 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, D.276 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.299, 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 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:P.138, E:Q.140 GOL.17: 4 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, Y.83 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:F.281, E:Q.63, E:Y.83 GOL.22: 3 residues within 4Å: Chain E: P.118, D.119 Chain G: T.3 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.119, E:D.119 GOL.24: 6 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, D.276 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:D.276, E:Q.299

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.7, CIJ.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.3, H2O.3 MG.7: 5 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: MG.6, CIJ.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.3 MG.18: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.19, CIJ.20 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.14, H2O.14 MG.19: 5 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: MG.18, CIJ.20 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.14

2 x CIJ: 2-(3-chloro-4-fluorobenzyl)-4,5-dihydroxy-1H-isoindole-1,3(2H)-dione(Non-covalent)

CIJ.8: 10 residues within 4Å: Chain A: D.131, D.188, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.6, MG.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.217, A:P.217 Hydrogen bonds: A:D.131 Water bridges: A:D.131, A:Y.132, A:N.227 CIJ.20: 10 residues within 4Å: Chain E: D.131, D.188, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.18, MG.19 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:P.217, E:P.217 Hydrogen bonds: E:D.131, E:D.188 Water bridges: E:Y.132, E:N.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Metifiot, M. et al., Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase. Acs Chem.Biol. (2013)

Release Date

2012-10-31

Peptides

INTEGRASE: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

INTEGRASE

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