SMTL ID : 9c9m.1

HIV-1 intasome core bound with DTG

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-2-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.134, D.186 Ligands: MG.2, DLU.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.134, A:D.186, H2O.1, H2O.1 MG.2: 6 residues within 4Å: Chain A: D.134, C.135, E.222, N.225 Ligands: MG.1, DLU.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.134, A:E.222, A:E.222, H2O.2 MG.5: 4 residues within 4Å: Chain F: D.134, D.186 Ligands: MG.6, DLU.8 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.134, F:D.186, H2O.2, H2O.2 MG.6: 5 residues within 4Å: Chain F: D.134, E.222, N.225 Ligands: MG.5, DLU.8 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.134, F:E.222, F:E.222, H2O.3

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.82, H.86, C.110, C.113 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.82, A:H.86, A:C.110, A:C.113 ZN.7: 4 residues within 4Å: Chain F: H.82, H.86, C.110, C.113 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.82, F:H.86, F:C.110, F:C.113

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.134, D.186, N.187, G.188, Y.213, P.215, Q.216, E.222 Chain D: G.4 Chain E: C.24, A.25 Ligands: MG.1, MG.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.222 Hydrogen bonds: A:D.186 Water bridges: A:C.135, A:N.187 DLU.8: 13 residues within 4Å: Chain F: D.134, D.186, N.187, G.188, Y.213, P.215, Q.216, E.222 Chain I: G.4 Chain J: C.24, A.25 Ligands: MG.5, MG.6 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:E.222 Hydrogen bonds: F:D.186 Water bridges: F:C.135, F:N.187, F:N.225, F:N.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., HIV-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies by Cryo-EM and Reveal the Role of the Integrase C-Terminal Tail in HIV-1 Integration. Viruses (2024)

Release Date

2024-07-31

Peptides

Integrase: ABFGKL
Integrase: CH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

F
I

G
K

K
L

L
C

C
D

H
M

Integrase

Integrase