SMTL ID : 5oi2.1

Dissociation of biochemical and antiretroviral activities of Integrase-LEDGF Allosteric Inhibitors revealed by resistance of A125 polymorphic HIV-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.34, C.35, N.87, N.90 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.34 MG.2: 6 residues within 4Å: Chain A: P.28, G.29, W.31, H.48, P.79, I.174 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:P.28, A:P.79 MG.3: 7 residues within 4Å: Chain A: Y.53, I.54, E.55, V.150, N.154 Chain B: G.76, R.77 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.54, H2O.5 MG.4: 6 residues within 4Å: Chain A: E.57, V.58, K.143, V.146, Q.147 Chain B: Y.69 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.69, H2O.4 MG.8: 4 residues within 4Å: Chain B: D.34, C.35, N.87, N.90 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.34 MG.9: 6 residues within 4Å: Chain B: P.28, G.29, W.31, H.48, P.79, I.174 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:P.28, B:P.79 MG.10: 7 residues within 4Å: Chain A: G.76, R.77 Chain B: Y.53, I.54, E.55, V.150, N.154 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.54, H2O.2 MG.11: 6 residues within 4Å: Chain A: Y.69 Chain B: E.57, V.58, K.143, V.146, Q.147 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.69, H2O.1

2 x 9VN: (2~{S})-2-[4-(4,4-dimethylcyclohexen-1-yl)-2-methyl-5-pyridin-4-yl-thiophen-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid(Non-covalent)

9VN.5: 11 residues within 4Å: Chain A: Q.65, L.72, T.94, T.95, A.98, A.99, W.102 Chain B: A.139, E.140, H.141, T.144 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Q.65, A:L.72, A:T.95, A:W.102 Hydrogen bonds: B:E.140, B:H.141, B:T.144 Salt bridges: B:H.141 9VN.12: 11 residues within 4Å: Chain A: A.139, E.140, H.141, T.144 Chain B: Q.65, L.72, T.94, T.95, A.98, A.99, W.102 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.65, B:L.72, B:T.95, B:W.102 Hydrogen bonds: A:E.140, A:H.141, A:T.144, A:T.144 Salt bridges: A:H.141

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

SO4.6: 3 residues within 4Å: Chain A: T.36, H.37, K.129 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.37, A:H.37 Water bridges: A:N.125 Salt bridges: A:H.37, A:K.129 SO4.7: 5 residues within 4Å: Chain A: K.41, R.136, E.140, H.141, L.142 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.136, A:L.142 Water bridges: A:K.41, A:K.41, A:K.143 Salt bridges: A:K.41, A:H.141 SO4.13: 3 residues within 4Å: Chain B: T.36, H.37, K.129 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.37, B:H.37 Water bridges: B:N.125 Salt bridges: B:H.37, B:K.129 SO4.14: 5 residues within 4Å: Chain B: K.41, R.136, E.140, H.141, L.142 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.136, B:L.142 Water bridges: B:K.41, B:K.41, B:K.143 Salt bridges: B:K.41, B:H.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonnard, D. et al., Structure-function analyses unravel distinct effects of allosteric inhibitors of HIV-1 integrase on viral maturation and integration. J. Biol. Chem. (2018)

Release Date

2018-03-07

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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