SMTL ID : 4id1.1

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x LF0: (2S)-tert-butoxy[4-(3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid(Non-covalent)

LF0.1: 13 residues within 4Å: Chain A: Q.46, L.53, T.75, T.76, A.79, A.80, W.83 Chain B: Q.119, A.120, E.121, H.122, T.125, M.129 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Q.46, A:A.79, A:W.83 Water bridges: A:Q.46 Hydrogen bonds: B:E.121, B:H.122, B:T.125 Salt bridges: B:H.122 LF0.5: 13 residues within 4Å: Chain A: Q.119, A.120, E.121, H.122, T.125, M.129 Chain B: Q.46, L.53, T.75, T.76, A.79, A.80, W.83 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.121, A:H.122, A:H.122, B:T.76 Salt bridges: A:H.122 Hydrophobic interactions: B:Q.46, B:A.79, B:W.83 Water bridges: B:Q.46

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

SO4.2: 5 residues within 4Å: Chain A: G.45, Q.46, S.74, T.75, T.76 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.45, A:Q.46, A:S.74, A:S.74, A:T.75, A:T.76 Water bridges: A:Q.46 SO4.3: 5 residues within 4Å: Chain A: K.22, R.117, E.121, H.122, L.123 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.117, A:L.123 Water bridges: A:K.22, A:K.22, A:K.124 Salt bridges: A:K.22, A:H.122 SO4.4: 3 residues within 4Å: Chain A: T.17, H.18, K.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.18, A:H.18 Salt bridges: A:H.18, A:K.110 SO4.6: 5 residues within 4Å: Chain B: G.45, Q.46, S.74, T.75, T.76 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.45, B:Q.46, B:S.74, B:S.74, B:T.75, B:T.76 Water bridges: B:Q.46 SO4.7: 5 residues within 4Å: Chain B: K.22, R.117, E.121, H.122, L.123 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.117, B:L.123 Water bridges: B:K.22, B:K.22, B:K.124 Salt bridges: B:K.22, B:H.122 SO4.8: 3 residues within 4Å: Chain B: T.17, H.18, K.110 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.18, B:H.18 Salt bridges: B:H.18, B:K.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jurado, K.A. et al., Allosteric integrase inhibitor potency is determined through the inhibition of HIV-1 particle maturation. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-05-01

Peptides

Gag-Pol polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Gag-Pol polyprotein

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