SMTL ID : 4e7k.1

PFV integrase Target Capture Complex (TCC-Mn), freeze-trapped prior to strand transfer, at 3.0 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.02 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.7: 4 residues within 4Å: Chain F: H.65, H.69, C.99, C.102 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.65, F:H.69, F:C.99, F:C.102

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 7 residues within 4Å: Chain A: D.131, Y.132, E.224, N.227 Chain D: A.17 Chain E: C.14 Ligands: MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.131, A:E.224, A:E.224 MN.3: 5 residues within 4Å: Chain A: D.131, D.188 Chain E: G.13, C.14 Ligands: MN.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.131, A:D.188 MN.4: 3 residues within 4Å: Chain B: D.131, Y.132, D.188 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.131, B:D.188, H2O.1, H2O.1, H2O.1 MN.8: 7 residues within 4Å: Chain F: D.131, Y.132, E.224, N.227 Chain I: A.17 Chain J: C.14 Ligands: MN.9 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.131, F:E.224, F:E.224 MN.9: 5 residues within 4Å: Chain F: D.131, D.188 Chain J: G.13, C.14 Ligands: MN.8 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.131, F:D.188 MN.10: 3 residues within 4Å: Chain G: D.131, Y.132, D.188 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.131, G:D.188, H2O.1, H2O.1, H2O.1

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

SO4.5: 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 SO4.11: 5 residues within 4Å: Chain G: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:V.263 Salt bridges: G:K.222, G:R.225

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain E: T.15, A.16 Chain J: T.15, A.16 Ligands: PGE.12 No protein-ligand interaction detected (PLIP) PGE.12: 5 residues within 4Å: Chain E: T.15, A.16 Chain J: T.15, A.16 Ligands: PGE.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hare, S. et al., 3'-Processing and strand transfer catalysed by retroviral integrase in crystallo. Embo J. (2012)

Release Date

2012-05-23

Peptides

Pro-Pol polyprotein: ABFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

F
A

G
B

Pro-Pol polyprotein

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