SMTL ID : 3oy9.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese at 2.55 resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 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.12: 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: 4 residues within 4Å: Chain A: D.131, D.188 Chain D: A.17 Ligands: MN.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.1 MN.3: 4 residues within 4Å: Chain A: D.131, E.224 Chain D: A.17 Ligands: MN.2 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 MN.10: 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.7, H2O.7, H2O.9 MN.13: 4 residues within 4Å: Chain E: D.131, D.188 Chain H: A.17 Ligands: MN.14 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.11, H2O.11 MN.14: 4 residues within 4Å: Chain E: D.131, E.224 Chain H: A.17 Ligands: MN.13 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.11 MN.21: 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.17, H2O.18, H2O.19

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

SO4.4: 2 residues within 4Å: Chain A: H.341, K.342 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.342 Salt bridges: A:H.341, A:K.342 SO4.11: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.263 Salt bridges: B:K.222, B:R.225 SO4.15: 2 residues within 4Å: Chain E: H.341, K.342 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.342 Salt bridges: E:H.341, E:K.342 SO4.22: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.263 Salt bridges: F:K.222, F:R.225

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.6: 3 residues within 4Å: Chain A: S.139, Q.140, K.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.140 GOL.7: 5 residues within 4Å: Chain A: L.295, Q.299 Chain B: Q.270, I.275, D.276 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.299, B:Q.270, B:D.276 GOL.8: 4 residues within 4Å: Chain A: Q.63, Y.83 Chain E: P.280, F.281 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:F.281, A:Q.63, A:Y.83 GOL.16: 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.17: 3 residues within 4Å: Chain E: S.139, Q.140, K.244 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.140 GOL.18: 5 residues within 4Å: Chain E: L.295, Q.299 Chain F: Q.270, I.275, D.276 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Q.270, F:D.276, E:Q.299 GOL.19: 4 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, Y.83 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Q.63, E:Y.83, E:Y.83, A:F.281

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

NH4.9: 2 residues within 4Å: Chain A: D.119 Chain C: T.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.119 NH4.20: 2 residues within 4Å: Chain E: D.119 Chain G: T.3 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hare, S. et al., Retroviral intasome assembly and inhibition of DNA strand transfer. Nature (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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