SMTL ID : 6l0c.1

Crystal structure of HIV-1 Integrase catalytic core domain (A128T/K173Q/F185K)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: T.24, H.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.25 Salt bridges: A:H.25, A:K.117 SO4.2: 2 residues within 4Å: Chain A: K.118, Q.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.122 Salt bridges: A:K.118, A:K.144 SO4.3: 5 residues within 4Å: Chain A: K.29, R.124, E.128, H.129, L.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.130 Water bridges: A:Q.131 Salt bridges: A:K.29, A:H.129 SO4.4: 3 residues within 4Å: Chain A: E.50, T.51, G.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.50, A:G.52 SO4.7: 2 residues within 4Å: Chain B: T.24, H.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.25 Salt bridges: B:H.25, B:K.117 SO4.8: 2 residues within 4Å: Chain B: K.118, Q.122 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.122 Salt bridges: B:K.118, B:K.144 SO4.9: 5 residues within 4Å: Chain B: K.29, R.124, E.128, H.129, L.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.130 Water bridges: B:Q.131 Salt bridges: B:K.29, B:H.129 SO4.10: 3 residues within 4Å: Chain B: E.50, T.51, G.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.50, B:G.52

4 x ARS: ARSENIC(Non-covalent)

ARS.5: 2 residues within 4Å: Chain A: C.23, N.78 No protein-ligand interaction detected (PLIP) ARS.6: 2 residues within 4Å: Chain A: C.88, Q.95 No protein-ligand interaction detected (PLIP) ARS.11: 2 residues within 4Å: Chain B: C.23, N.78 No protein-ligand interaction detected (PLIP) ARS.12: 2 residues within 4Å: Chain B: C.88, Q.95 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, T. et al., A Conformational Escape Reaction of HIV-1 against an Allosteric Integrase Inhibitor. J.Virol. (2020)

Release Date

2020-07-01

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase