SMTL ID : 3l2r.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 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.10: 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 MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.131, D.188 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.131, A:D.188 MG.8: 3 residues within 4Å: Chain B: D.131, Y.132, D.188 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.131, B:D.188 MG.11: 2 residues within 4Å: Chain E: D.131, D.188 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.131, E:D.188 MG.17: 3 residues within 4Å: Chain F: D.131, Y.132, 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)

NH4.3: 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 NH4.12: 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

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: S.165, T.166, S.167, S.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.166, A:T.166, A:S.167, A:S.167 GOL.5: 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, A:T.243 GOL.6: 3 residues within 4Å: Chain A: T.194, F.211 Chain C: T.2 No protein-ligand interaction detected (PLIP) GOL.7: 3 residues within 4Å: Chain A: H.341, K.342, H.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.342 GOL.9: 7 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, I.275, D.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.276 GOL.13: 4 residues within 4Å: Chain E: S.165, T.166, S.167, S.195 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.166, E:T.166, E:S.167, E:S.167 GOL.14: 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, E:T.243 GOL.15: 3 residues within 4Å: Chain E: T.194, F.211 Chain G: T.2 No protein-ligand interaction detected (PLIP) GOL.16: 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.18: 7 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, I.275, D.276 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.276

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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