SMTL ID : 5hrp.1

HIV Integrase Catalytic Domain containing F185K + A124T mutations complexed with GSK0002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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.11: 4 residues within 4Å: Chain B: C.17, E.44, T.49, N.72 No protein-ligand interaction detected (PLIP) CAC.12: 5 residues within 4Å: Chain B: K.79, C.82, I.87, K.88, Q.89 No protein-ligand interaction detected (PLIP)

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

SO4.3: 5 residues within 4Å: Chain A: K.23, R.118, E.122, H.123, L.124 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.122, A:L.124 Water bridges: A:E.21, A:K.23, A:K.125 Salt bridges: A:K.23, A:H.123 SO4.4: 3 residues within 4Å: Chain B: A.80, W.83 Ligands: 65P.10 No protein-ligand interaction detected (PLIP) SO4.5: 2 residues within 4Å: Chain A: K.112, Q.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.116 Salt bridges: A:K.112 SO4.6: 3 residues within 4Å: Chain A: C.17, T.18, H.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.19, A:H.19 Water bridges: A:C.17, A:T.18 SO4.13: 5 residues within 4Å: Chain B: K.23, R.118, E.122, H.123, L.124 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.122, B:L.124 Water bridges: B:K.23, B:K.23, B:E.122, B:K.125 Salt bridges: B:K.23, B:H.123 SO4.14: 3 residues within 4Å: Chain A: A.80, W.83 Ligands: 65P.20 No protein-ligand interaction detected (PLIP) SO4.15: 2 residues within 4Å: Chain B: K.112, Q.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.116 Salt bridges: B:K.112 SO4.16: 3 residues within 4Å: Chain B: C.17, T.18, H.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.18, B:H.19, B:H.19 Water bridges: B:C.17

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

EDO.7: 3 residues within 4Å: Chain A: S.75, T.76, T.77 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.76, A:T.76, A:T.76, A:T.77, A:T.77 Water bridges: A:Q.47 EDO.8: 2 residues within 4Å: Chain A: D.119, Q.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.119 Water bridges: A:Q.120, A:Q.120 EDO.9: 4 residues within 4Å: Chain A: R.118, D.119, A.121, E.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.118, A:R.118, A:D.119 EDO.17: 3 residues within 4Å: Chain B: S.75, T.76, T.77 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.76, B:T.76, B:T.77, B:T.77 Water bridges: B:Q.47 EDO.18: 2 residues within 4Å: Chain B: D.119, Q.120 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.119 Water bridges: B:Q.120, B:Q.120 EDO.19: 4 residues within 4Å: Chain B: R.118, D.119, A.121, E.122 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.118, B:R.118, B:D.119

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.10: 14 residues within 4Å: Chain A: Q.120, A.121, E.122, H.123, T.126, M.130 Chain B: Q.47, L.54, T.76, T.77, A.80, A.81, W.84 Ligands: SO4.4 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.126, B:Q.47, B:A.80, B:W.84 Hydrogen bonds: A:E.122, A:H.123 Water bridges: A:E.122, B:Q.47 Salt bridges: A:H.123 65P.20: 14 residues within 4Å: Chain A: Q.47, L.54, T.76, T.77, A.80, A.81, W.84 Chain B: Q.120, A.121, E.122, H.123, T.126, M.130 Ligands: SO4.14 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.126, A:Q.47, A:A.80, A:W.84 Hydrogen bonds: B:E.122, B:H.123, 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