SMTL ID : 5hrs.1

HIV Integrase Catalytic Domain containing F185K + A124N + T125A mutations complexed with GSK0002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

4 x CAC: CACODYLATE ION(Non-covalent)

CAC.1: 4 residues within 4Å: Chain A: C.17, E.44, T.49, N.72 No protein-ligand interaction detected (PLIP) CAC.2: 6 residues within 4Å: Chain A: V.78, K.79, C.82, I.87, K.88, Q.89 No protein-ligand interaction detected (PLIP) CAC.7: 4 residues within 4Å: Chain B: C.17, E.44, T.49, N.72 No protein-ligand interaction detected (PLIP) CAC.8: 6 residues within 4Å: Chain B: V.78, K.79, C.82, I.87, K.88, Q.89 No protein-ligand interaction detected (PLIP)

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

SO4.3: 6 residues within 4Å: Chain A: E.21, K.23, R.118, E.122, H.123, L.124 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.118, A:E.122, A:L.124 Water bridges: A:K.125 Salt bridges: A:K.23, A:H.123 SO4.4: 2 residues within 4Å: Chain A: N.76 Ligands: 65P.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.76 Water bridges: A:N.76, A:N.76 SO4.9: 6 residues within 4Å: Chain B: E.21, K.23, R.118, E.122, H.123, L.124 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.118, B:E.122, B:L.124 Water bridges: B:K.125 Salt bridges: B:K.23, B:H.123 SO4.10: 2 residues within 4Å: Chain B: N.76 Ligands: 65P.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.76 Water bridges: B:N.76, B:N.76

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: G.58, R.59, W.60, P.61 Chain B: N.136, K.137, G.149 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:E.150, B:E.150 Hydrogen bonds: A:G.58 EDO.11: 7 residues within 4Å: Chain A: N.136, K.137, G.149 Chain B: G.58, R.59, W.60, P.61 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.150, A:E.150 Hydrogen bonds: B:G.58

2 x 65P: (2S)-tert-butoxy[1-(3,4-difluorobenzyl)-6-methyl-4-(5-methyl-3,4-dihydro-2H-chromen-6-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]acetic acid(Non-covalent)

65P.6: 14 residues within 4Å: Chain A: Q.120, A.121, E.122, H.123, T.126, M.130 Chain B: Q.47, L.54, N.76, A.77, A.80, A.81, W.84 Ligands: SO4.10 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.47, B:A.80, B:A.81, B:W.84, A:T.126 Water bridges: B:Q.47 Hydrogen bonds: A:E.122, A:H.123 Salt bridges: A:H.123 65P.12: 14 residues within 4Å: Chain A: Q.47, L.54, N.76, A.77, A.80, A.81, W.84 Chain B: Q.120, A.121, E.122, H.123, T.126, M.130 Ligands: SO4.4 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.47, A:A.80, A:A.81, A:W.84, B:T.126 Water bridges: A:Q.47 Hydrogen bonds: B:E.122, B:H.123, B:T.126 Salt bridges: B:H.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, K. et al., Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase. PLoS Biol. (2016)

Release Date

2016-12-14

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase