SMTL ID : 8buv.1

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-tetramer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.1, H2O.2, H2O.2, H2O.3 MG.8: 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.4, H2O.4, H2O.5, H2O.6

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

EDO.2: 2 residues within 4Å: Chain B: H.88, K.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.87, B:T.87, B:H.88 EDO.3: 3 residues within 4Å: Chain B: V.93, A.112, E.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.113 Water bridges: B:G.91, B:E.113 EDO.4: 2 residues within 4Å: Chain B: G.184, R.187 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain B: K.92, V.109, H.192, L.193, K.194 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.193, B:K.194 Water bridges: B:K.92 EDO.7: 6 residues within 4Å: Chain B: D.188, Q.189, A.190, E.191 Chain C: K.48 Ligands: 723.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.48 EDO.9: 6 residues within 4Å: Chain D: E.113, T.114, G.115, S.140, N.141, S.144 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.115 Water bridges: D:Q.116

2 x 723: (6-chloro-2-oxo-4-phenyl-1,2-dihydroquinolin-3-yl)acetic acid(Non-covalent)

723.6: 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, T.145, T.146, A.149, A.150 Ligands: EDO.7 11 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: B:T.195, D:T.146 Hydrogen bonds: B:E.191, B:H.192, D:Q.116 Salt bridges: B:H.192 Water bridges: C:K.48, C:K.48 pi-Stacking: C:W.17 pi-Cation interactions: C:K.48, C:K.48 723.10: 15 residues within 4Å: Chain A: Y.8, W.17, K.48, I.50 Chain B: Q.116, T.145, T.146, A.149, A.150 Chain D: Q.189, A.190, E.191, H.192, T.195, M.199 20 PLIP interactions: 6 interactions with chain D, 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: D:E.191, D:H.192, D:T.195, D:T.195, B:Q.116 Water bridges: D:H.192, A:K.48, A:K.48, B:Q.116, B:T.146 Salt bridges: D:H.192, A:K.48 Hydrophobic interactions: A:K.48, A:K.48, A:I.50, B:T.146, B:A.149 pi-Stacking: A:W.17, A:W.17 pi-Cation interactions: A:K.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singer, M.R. et al., HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3. To Be Published

Release Date

2023-12-13

Peptides

Integrase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Integrase

Related Entries With Identical Sequence