SMTL ID : 7jn3.1

Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.9, A:H.13, A:C.37, A:C.40 ZN.5: 4 residues within 4Å: Chain E: H.9, H.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.9, E:H.13, E:C.37, E:C.40

2 x ZZX: (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide(Non-covalent)

ZZX.2: 10 residues within 4Å: Chain A: D.64, D.121, S.150, Q.151, E.157 Chain I: G.4 Chain J: C.15, A.16 Ligands: MG.3, MG.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.157 Hydrogen bonds: A:S.150 Salt bridges: A:D.121 ZZX.6: 10 residues within 4Å: Chain E: D.64, D.121, S.150, Q.151, E.157 Chain K: G.4 Chain L: C.15, A.16 Ligands: MG.7, MG.8 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.150

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.64, E.157 Ligands: ZZX.2, MG.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.64, A:D.64, A:E.157, A:E.157 MG.4: 4 residues within 4Å: Chain A: D.64, D.121 Ligands: ZZX.2, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.64, A:D.121, A:D.121 MG.7: 4 residues within 4Å: Chain E: D.64, D.121 Ligands: ZZX.6, MG.8 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.64, E:D.121, E:D.121 MG.8: 6 residues within 4Å: Chain E: D.64, D.121, Q.153, E.157 Ligands: ZZX.6, MG.7 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.64, E:D.64, E:E.157, E:E.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, K.K. et al., Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome. Commun Biol (2021)

Release Date

2021-03-17

Peptides

integrase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

integrase

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