SMTL ID : 8w2r.1

HIV-1 P5-IN intasome core

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.138, D.190 Ligands: MG.2, DLU.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.138, A:D.190 MG.2: 4 residues within 4Å: Chain A: D.138, E.226 Ligands: MG.1, DLU.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.138, A:E.226, A:E.226 MG.5: 4 residues within 4Å: Chain G: D.138, D.190 Ligands: MG.6, DLU.8 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.138, G:D.190 MG.6: 5 residues within 4Å: Chain G: D.138, E.226, N.229 Ligands: MG.5, DLU.8 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.138, G:E.226, G:E.226

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.86, H.90, C.114, C.117 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.86, A:H.90, A:C.114, A:C.117 ZN.7: 4 residues within 4Å: Chain G: H.86, H.90, C.114, C.117 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.86, G:H.90, G:C.114, G:C.117

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: 12 residues within 4Å: Chain A: D.138, D.190, N.191, G.192, P.219, Q.220, E.226 Chain E: G.4 Chain F: C.24, A.25 Ligands: MG.1, MG.2 1 PLIP interactions: 1 interactions with chain A Halogen bonds: A:E.226 DLU.8: 12 residues within 4Å: Chain G: D.138, D.190, N.191, G.192, P.219, Q.220, E.226 Chain K: G.4 Chain L: C.24, A.25 Ligands: MG.5, MG.6 1 PLIP interactions: 1 interactions with chain G Halogen bonds: G:E.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro. J.Mol.Biol. (2024)

Release Date

2024-04-17

Peptides

Integrase: ABCDGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

G
I

H
K

I
L

J
M

Integrase