SMTL ID : 5fro.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ446 (compound 4f)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.67 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.16: 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 MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.3, XXJ.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.1 MG.3: 6 residues within 4Å: Chain A: D.131, E.224, N.227 Chain D: A.17 Ligands: MG.2, XXJ.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.1 MG.14: 2 residues within 4Å: Chain B: D.131, D.188 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.131, B:D.188 MG.17: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.18, XXJ.23 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.8, H2O.8 MG.18: 6 residues within 4Å: Chain E: D.131, E.224, N.227 Chain H: A.17 Ligands: MG.17, XXJ.23 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.8 MG.29: 2 residues within 4Å: Chain F: D.131, D.188 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.131, F:D.188

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

SO4.4: 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:Q.140, A:Q.140 Salt bridges: A:K.244 SO4.5: 3 residues within 4Å: Chain A: G.190, A.191 Ligands: XXJ.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.191 Water bridges: A:A.192, A:A.192 SO4.6: 4 residues within 4Å: Chain A: S.335, L.336, R.339 Chain E: K.231 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.335, A:L.336 Salt bridges: A:R.339, E:K.231 SO4.7: 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 SO4.11: 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 SO4.19: 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:Q.140, E:Q.140 Salt bridges: E:K.244 SO4.20: 3 residues within 4Å: Chain E: G.190, A.191 Ligands: XXJ.23 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:A.191 Water bridges: E:A.192, E:A.192 SO4.21: 4 residues within 4Å: Chain A: K.231 Chain E: S.335, L.336, R.339 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.335, E:L.336 Salt bridges: E:R.339, A:K.231 SO4.22: 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 SO4.26: 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

2 x XXJ: 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide(Non-covalent)

XXJ.8: 14 residues within 4Å: Chain A: D.131, D.188, Q.189, G.190, Y.215, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.2, MG.3, SO4.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.188, A:Y.215, A:P.217, A:P.217 Water bridges: A:D.131, A:Y.132, A:E.224, A:E.224, A:N.227 Halogen bonds: A:E.224 XXJ.23: 14 residues within 4Å: Chain E: D.131, D.188, Q.189, G.190, Y.215, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.17, MG.18, SO4.20 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:D.188, E:Y.215, E:P.217, E:P.217 Hydrogen bonds: E:D.188 Water bridges: E:Y.132, E:N.227 Halogen bonds: E:E.224

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: S.165, T.166, S.167 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.166, A:T.166 GOL.10: 5 residues within 4Å: Chain A: R.117, Y.306, P.308 Chain C: C.6 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.117, A:R.117, A:Y.306 GOL.12: 7 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, I.275, D.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.270, B:D.276, B:D.276 GOL.13: 6 residues within 4Å: Chain A: S.178 Chain B: L.158, P.160, Y.246, P.250, Q.253 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.158, B:Y.246, B:Q.253, A:S.178 GOL.15: 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: GOL.10 No protein-ligand interaction detected (PLIP) GOL.24: 3 residues within 4Å: Chain E: S.165, T.166, S.167 2 PLIP interactions: 2 interactions with chain E Water bridges: E:T.166, E:T.166 GOL.25: 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 Hydrogen bonds: E:R.117, E:R.117 GOL.27: 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 GOL.28: 6 residues within 4Å: Chain E: S.178 Chain F: L.158, P.160, Y.246, P.250, Q.253 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:L.158, F:Y.246, F:Q.253, E:S.178 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: GOL.25 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, X.Z. et al., HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases. Acs Chem.Biol. (2016)

Release Date

2016-02-17

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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