SMTL ID : 3l2w.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese and GS9137 (Elvitegravir)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 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.11: 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: 3 residues within 4Å: Chain A: D.131, D.188 Ligands: ELV.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.131, A:D.188 MN.3: 4 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: ELV.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.131, A:E.224, A:E.224 MN.10: 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 MN.12: 3 residues within 4Å: Chain E: D.131, D.188 Ligands: ELV.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.131, E:D.188 MN.13: 4 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: ELV.15 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.131, E:E.224, E:E.224 MN.20: 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

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

NH4.4: 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 NH4.14: 2 residues within 4Å: Chain E: D.119 Chain G: T.3 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.119, E:D.119, E:D.119

2 x ELV: 6-(3-chloro-2-fluorobenzyl)-1-[(1S)-1-(hydroxymethyl)-2-methylpropyl]-7-methoxy-4-oxo-1,4-dihydroquinoline-3-carboxylic acid(Non-covalent)

ELV.5: 12 residues within 4Å: Chain A: D.131, D.188, Y.215, H.216, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MN.2, MN.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.215, A:P.217, A:P.217, A:E.224 ELV.15: 12 residues within 4Å: Chain E: D.131, D.188, Y.215, H.216, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MN.12, MN.13 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Y.215, E:P.217, E:P.217, E:E.224

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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:Q.140, A:T.243 GOL.7: 4 residues within 4Å: Chain A: Q.189, T.194, F.211 Chain C: T.2 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain A: H.341, K.342, H.360 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.342, A:H.360 GOL.9: 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.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:Q.140, E:T.243 GOL.17: 4 residues within 4Å: Chain E: Q.189, T.194, F.211 Chain G: T.2 No protein-ligand interaction detected (PLIP) GOL.18: 3 residues within 4Å: Chain E: H.341, K.342, H.360 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.341, E:K.342, E:H.360 GOL.19: 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

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

2010-02-09

Peptides

Integrase: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

Integrase

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