SMTL ID : 1k6y.2 (3 other biounits)

Crystal Structure of a Two-Domain Fragment of HIV-1 Integrase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.12, H.16, C.40, C.43 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.12, A:H.16, A:C.40, A:C.43 ZN.4: 4 residues within 4Å: Chain B: H.12, H.16, C.40, C.43 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.12, B:H.16, B:C.40, B:C.43 ZN.7: 4 residues within 4Å: Chain C: H.12, H.16, C.40, C.43 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.12, C:H.16, C:C.40, C:C.43 ZN.10: 4 residues within 4Å: Chain D: H.12, H.16, C.40, C.43 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.12, D:H.16, D:C.40, D:C.43

4 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: V.37, A.38, C.40, C.43 No protein-ligand interaction detected (PLIP) K.5: 5 residues within 4Å: Chain B: V.37, A.38, C.40, C.43, Q.44 No protein-ligand interaction detected (PLIP) K.8: 4 residues within 4Å: Chain C: V.37, A.38, C.40, C.43 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.43 K.11: 4 residues within 4Å: Chain D: V.37, A.38, C.40, C.43 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:C.40

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: C.65, T.66, H.67, N.155, K.159 Chain D: H.171 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:H.67, A:N.155 Water bridges: A:C.65, D:H.171 Salt bridges: A:H.67, A:K.159, D:H.171 PO4.6: 4 residues within 4Å: Chain B: C.65, T.66, H.67, K.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.66, B:H.67 Salt bridges: B:H.67, B:K.159 PO4.9: 4 residues within 4Å: Chain C: C.65, T.66, H.67, K.159 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.67, C:H.67 Water bridges: C:C.65, C:T.66 Salt bridges: C:H.67, C:K.159 PO4.12: 5 residues within 4Å: Chain D: C.65, T.66, H.67, N.155, K.159 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.66, D:T.66, D:H.67 Water bridges: D:C.65 Salt bridges: D:H.67, D:K.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J.Y. et al., Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein. EMBO J. (2001)

Release Date

2001-12-21

Peptides

Integrase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Integrase

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