SMTL ID : 8fnq.1

Structure of E138K/G140A/Q148K HIV-1 intasome with 4d bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

2 x OZ1: 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide(Non-covalent)

OZ1.1: 13 residues within 4Å: Chain A: D.140, D.192, N.193, P.218, Y.219, P.221, Q.222, E.228 Chain E: G.4 Chain F: C.24, A.25 Ligands: MG.2, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.228 Hydrogen bonds: A:E.228 Water bridges: A:C.141, A:N.193 Halogen bonds: A:E.228 OZ1.5: 13 residues within 4Å: Chain G: D.140, D.192, N.193, P.218, Y.219, P.221, Q.222, E.228 Chain K: G.4 Chain L: C.24, A.25 Ligands: MG.6, MG.7 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:E.228 Hydrogen bonds: G:E.228 Water bridges: G:C.141, G:N.193 Halogen bonds: G:E.228

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.140, D.192 Ligands: OZ1.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.140, A:D.192, H2O.1, H2O.2 MG.3: 5 residues within 4Å: Chain A: D.140, E.228, N.231 Ligands: OZ1.1, MG.2 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.6: 4 residues within 4Å: Chain G: D.140, D.192 Ligands: OZ1.5, MG.7 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.140, G:D.192, H2O.7, H2O.8 MG.7: 5 residues within 4Å: Chain G: D.140, E.228, N.231 Ligands: OZ1.5, MG.6 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.140, G:E.228, G:E.228, H2O.8

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.8: 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

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, isoform alpha,Integrase chimera: 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, isoform alpha,Integrase chimera

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