SMTL ID : 3s3m.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and Dolutegravir (S/GSK1349572)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 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 SO4.11: 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 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.342 Salt bridges: E:H.341, E:K.342, E:H.360 SO4.23: 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.165, T.166, S.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.166, A:T.166, A:S.167, 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:Q.140, A:Q.140 Water bridges: A:G.141 GOL.5: 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.6: 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 E, 1 interactions with chain A Hydrogen bonds: E:F.281, A:Y.83 GOL.15: 3 residues within 4Å: Chain E: S.165, T.166, S.167 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.166, E:S.167, 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:Q.140, E:Q.140 Water bridges: E:G.141 GOL.17: 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.18: 5 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, L.82, Y.83 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:F.281, E:Y.83, E:Y.83

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

NH4.7: 2 residues within 4Å: Chain A: P.118, D.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.119, A:D.119 NH4.19: 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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.9, DLU.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.5 MG.9: 5 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: MG.8, DLU.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.9 MG.20: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.21, DLU.22 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.10, H2O.14 MG.21: 5 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: MG.20, DLU.22 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.18

2 x DLU: (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide(Non-covalent)

DLU.10: 14 residues within 4Å: Chain A: D.131, D.188, Q.189, G.190, Y.215, P.217, Q.218, E.224, R.332 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.8, MG.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.217, A:P.217 Water bridges: A:D.131, A:Y.132, A:Y.215, A:H.216, A:N.227, A:R.332 DLU.22: 14 residues within 4Å: Chain E: D.131, D.188, Q.189, G.190, Y.215, P.217, Q.218, E.224, R.332 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.20, MG.21 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:P.217, E:P.217 Water bridges: E:Y.132, E:Y.215, E:H.216, E:N.227, E:R.332

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

HEZ.12: 6 residues within 4Å: Chain A: S.178 Chain B: L.158, Y.159, Y.246, P.250, Q.253 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.159 Hydrogen bonds: B:L.158, B:Y.246, B:Q.253 HEZ.24: 6 residues within 4Å: Chain E: S.178 Chain F: L.158, Y.159, Y.246, P.250, Q.253 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Y.159 Hydrogen bonds: F:L.158, F:Y.246, F:Q.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hare, S. et al., Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572). Mol.Pharmacol. (2011)

Release Date

2011-07-13

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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