SMTL ID : 3oym.1

Crystal structure of the PFV N224H mutant intasome bound to manganese

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 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.15: 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 MN: MANGANESE (II) ION(Non-covalent)

MN.2: 2 residues within 4Å: Chain A: D.131, D.188 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.1, H2O.8, H2O.8 MN.8: 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.13, H2O.17, H2O.17 MN.10: 2 residues within 4Å: Chain B: E.224, H.227 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.224, B:H.227, H2O.13, H2O.13, H2O.13 MN.16: 2 residues within 4Å: Chain E: D.131, D.188 6 PLIP interactions: 2 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.23, H2O.23, H2O.31, H2O.31 MN.22: 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.36, H2O.39, H2O.40 MN.24: 2 residues within 4Å: Chain F: E.224, H.227 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.224, F:H.227, H2O.36, H2O.36, H2O.36

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

SO4.3: 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 SO4.6: 4 residues within 4Å: Chain A: A.334, S.335, R.339 Chain E: K.231 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain A Water bridges: E:K.231, E:K.231, E:K.231, E:K.231, E:K.231, A:R.339, A:R.339 Salt bridges: E:K.231, A:R.339 Hydrogen bonds: A:A.334 SO4.12: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.261, B:S.261, B:V.263 Salt bridges: B:K.222, B:R.225 SO4.17: 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 SO4.20: 4 residues within 4Å: Chain A: K.231 Chain E: A.334, S.335, R.339 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain A Hydrogen bonds: E:A.334 Water bridges: E:R.339, E:R.339, A:K.231, A:K.231, A:K.231, A:K.231, A:K.231 Salt bridges: E:R.339, A:K.231 SO4.26: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.261, F:S.261, F:V.263 Salt bridges: F:K.222, F:R.225

10 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.7: 3 residues within 4Å: Chain A: S.139, Q.140, K.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.140 Water bridges: A:Q.140, A:G.141 GOL.9: 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: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.299, B:G.274, B:D.276 GOL.11: 10 residues within 4Å: Chain B: F.129, I.130, H.186, S.187, P.217, Q.218, S.219, S.220, V.223, E.224 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.130, B:I.130, B:H.186, B:S.219, B:S.220, B:S.220 Water bridges: B:D.188 GOL.14: 6 residues within 4Å: Chain A: V.263, Y.306 Chain C: C.6, A.7, T.8 Chain D: C.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.263, A:Y.306 GOL.18: 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.21: 3 residues within 4Å: Chain E: S.139, Q.140, K.244 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.140 Water bridges: E:Q.140, E:G.141 GOL.23: 7 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, I.275, D.276 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.274, F:D.276, E:Q.299 GOL.25: 10 residues within 4Å: Chain F: F.129, I.130, H.186, S.187, P.217, Q.218, S.219, S.220, V.223, E.224 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:I.130, F:I.130, F:H.186, F:S.219, F:S.220, F:S.220 Water bridges: F:D.188 GOL.28: 6 residues within 4Å: Chain E: V.263, Y.306 Chain G: C.6, A.7, T.8 Chain H: C.11 2 PLIP interactions: 2 interactions with chain E Water bridges: E:V.263, E:Y.306

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

NH4.5: 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

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

HEZ.13: 3 residues within 4Å: Chain B: L.136, K.231, T.235 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.136 Water bridges: B:G.134 HEZ.27: 3 residues within 4Å: Chain F: L.136, K.231, T.235 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.136 Water bridges: F:G.134

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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