SMTL ID : 8fnm.1

Structure of G140A/Q148K HIV-1 intasome with Dolutegravir bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.80 Å

Oligo State

homo-octamer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.140, D.192, K.224 Ligands: MG.2, DLU.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.140, A:D.192, H2O.1, H2O.1 MG.2: 5 residues within 4Å: Chain A: D.140, K.224, E.228 Ligands: MG.1, DLU.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.140, A:E.228, A:E.228, H2O.1 MG.5: 5 residues within 4Å: Chain G: D.140, D.192, K.224 Ligands: MG.6, DLU.8 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.140, G:D.192, H2O.9, H2O.9 MG.6: 5 residues within 4Å: Chain G: D.140, K.224, E.228 Ligands: MG.5, DLU.8 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.140, G:E.228, G:E.228, H2O.10

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.88, H.92, C.116, C.119 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.88, A:H.92, A:C.116, A:C.119 ZN.7: 4 residues within 4Å: Chain G: H.88, H.92, C.116, C.119 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.88, G:H.92, G:C.116, G:C.119

2 x DLU: (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide(Non-covalent)

DLU.4: 13 residues within 4Å: Chain A: D.140, D.192, G.194, Y.219, P.221, Q.222, K.224, E.228 Chain E: G.4 Chain F: C.24, A.25 Ligands: MG.1, MG.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.221 Hydrogen bonds: A:D.140, A:K.224 Water bridges: A:N.231 DLU.8: 13 residues within 4Å: Chain G: D.140, D.192, G.194, Y.219, P.221, Q.222, K.224, E.228 Chain K: G.4 Chain L: C.24, A.25 Ligands: MG.5, MG.6 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:P.221 Hydrogen bonds: G:D.140, G:K.224 Water bridges: G:N.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. Sci Adv (2023)

Release Date

2023-08-09

Peptides

Lamina-associated polypeptide 2, isoforms beta/gamma,Integrase: ABCDGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

G
G

H
H

I
I

J
J

Lamina-associated polypeptide 2, isoforms beta/gamma,Integrase