SMTL ID : 5hrr.1

HIV Integrase Catalytic Domain containing F185K + A124N + T125S mutations complexed with GSK0002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 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: 5 residues within 4Å: Chain A: K.79, C.82, I.87, K.88, Q.89 No protein-ligand interaction detected (PLIP) CAC.8: 4 residues within 4Å: Chain B: C.17, E.44, T.49, N.72 No protein-ligand interaction detected (PLIP) CAC.9: 5 residues within 4Å: Chain B: K.79, C.82, I.87, K.88, Q.89 No protein-ligand interaction detected (PLIP)

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

SO4.3: 5 residues within 4Å: Chain A: Q.47, S.75, N.76, S.77 Ligands: 65P.14 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.47, A:S.75, A:N.76, A:S.77 Water bridges: A:G.46, A:N.76, A:N.76 SO4.4: 5 residues within 4Å: Chain A: K.23, R.118, E.122, H.123, L.124 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.118, A:L.124 Water bridges: A:K.23, A:K.23, A:E.122, A:K.125 Salt bridges: A:K.23, A:H.123 SO4.5: 1 residues within 4Å: Chain A: H.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.19 SO4.10: 5 residues within 4Å: Chain B: Q.47, S.75, N.76, S.77 Ligands: 65P.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.47, B:S.75, B:N.76, B:S.77 Water bridges: B:G.46, B:N.76, B:N.76 SO4.11: 5 residues within 4Å: Chain B: K.23, R.118, E.122, H.123, L.124 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.118, B:L.124 Water bridges: B:K.23, B:K.23, B:E.122, B:E.122, B:K.125 Salt bridges: B:K.23, B:H.123 SO4.12: 1 residues within 4Å: Chain B: H.19 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.19

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

EDO.6: 4 residues within 4Å: Chain A: N.76, K.79, A.80, W.83 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.83 EDO.13: 4 residues within 4Å: Chain B: N.76, K.79, A.80, W.83 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.83

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.7: 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, S.77, A.80, A.81, W.84 Ligands: SO4.10 10 PLIP interactions: 5 interactions with chain B, 5 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, A:T.126 Salt bridges: A:H.123 65P.14: 14 residues within 4Å: Chain A: Q.47, L.54, N.76, S.77, A.80, A.81, W.84 Chain B: Q.120, A.121, E.122, H.123, T.126, M.130 Ligands: SO4.3 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.126, A:Q.47, A:A.80, A:A.81, A:W.84 Hydrogen bonds: B:E.122, B:H.123, B:T.126, B:T.126 Salt bridges: B:H.123 Water bridges: A:Q.47

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