SMTL ID : 8a1p.1

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor BI-D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: K.48, I.49 Chain D: D.188, Q.189, E.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.48, A:I.49, A:I.49 EDO.3: 6 residues within 4Å: Chain B: P.130, D.228, I.229, K.232 Chain D: E.219 Ligands: PEG.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.228, B:K.232, D:E.219 EDO.6: 5 residues within 4Å: Chain B: D.188, Q.189, A.190, E.191 Chain C: K.48 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.189, C:K.48

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 7 residues within 4Å: Chain B: V.109, P.111, E.117, Y.120 Chain D: V.109, K.194 Ligands: PEG.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:V.109, D:V.109 PEG.9: 4 residues within 4Å: Chain D: H.88, L.89, E.90, G.91 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.89, D:G.91 PEG.10: 9 residues within 4Å: Chain B: E.108, K.124, K.194 Chain D: E.108, V.109, P.111, E.117, K.124 Ligands: PEG.2 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.108, B:K.194, D:K.124 Water bridges: B:K.124 PEG.12: 4 residues within 4Å: Chain B: Q.116, E.117 Chain D: H.192, K.194 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.117, D:K.194 PEG.13: 7 residues within 4Å: Chain B: P.130 Chain D: K.206, R.208, S.216, G.218, E.219 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.216

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain B: V.186, Q.189 Chain C: Y.53 Chain D: W.153 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.189, D:W.153 GOL.8: 4 residues within 4Å: Chain A: Y.53 Chain B: W.153 Chain D: Q.189, I.203 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: D:Q.189, D:Q.189, B:W.153 Water bridges: A:R.51, A:R.51

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

LF0.5: 15 residues within 4Å: Chain B: Q.189, A.190, E.191, H.192, T.195, M.199 Chain C: Y.8, W.17, K.48 Chain D: Q.116, L.123, T.146, A.149, A.150, W.153 15 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: C:Y.8, C:W.17, C:K.48, D:A.149, D:A.149, D:A.150, D:W.153, B:T.195 Salt bridges: C:K.48, B:H.192 pi-Stacking: C:W.17 pi-Cation interactions: C:K.48 Hydrogen bonds: B:E.191, B:H.192, B:T.195 LF0.11: 15 residues within 4Å: Chain A: W.17, K.48, I.50 Chain B: Q.116, L.123, T.146, A.149, A.150, W.153 Chain D: Q.189, A.190, E.191, H.192, T.195, M.199 18 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: B:Q.116, B:T.146, B:A.149, B:A.149, B:A.150, B:W.153, A:K.48, A:I.50, D:T.195 Salt bridges: A:K.48, D:H.192 pi-Stacking: A:W.17, A:W.17 pi-Cation interactions: A:K.48 Hydrogen bonds: D:E.191, D:H.192, D:T.195, D:T.195

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain B: D.85, D.137 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.85, B:D.137, H2O.2, H2O.2, H2O.2, H2O.3 MG.14: 2 residues within 4Å: Chain D: D.85, D.137 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.85, D:D.137, H2O.5, H2O.5, H2O.5, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singer, M.R. et al., The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. Mbio (2023)

Release Date

2023-02-01

Peptides

Integrase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Integrase

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