SMTL ID : 6u8q.1

CryoEM structure of HIV-1 cleaved synaptic complex (CSC) intasome

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.140, C.141, D.192, E.228 Ligands: MG.2, DLU.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.140, A:D.140, A:D.192 MG.2: 4 residues within 4Å: Chain A: D.140, E.228 Ligands: MG.1, DLU.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.228, A:E.228 MG.4: 6 residues within 4Å: Chain E: D.140, C.141, D.192, E.228 Ligands: MG.5, DLU.6 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.140, E:D.192 MG.5: 4 residues within 4Å: Chain E: D.140, E.228 Ligands: MG.4, DLU.6 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.140, E:E.228, E:E.228

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.3: 10 residues within 4Å: Chain A: D.140, D.192, P.221, Q.222, E.228 Chain G: G.4 Chain H: C.24, A.25 Ligands: MG.1, MG.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.222 DLU.6: 10 residues within 4Å: Chain C: G.4 Chain D: C.24, A.25 Chain E: D.140, D.192, P.221, Q.222, E.228 Ligands: MG.4, MG.5 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:P.221 Hydrogen bonds: E:E.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., A Peptide Derived from Lens Epithelium-Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies. J.Mol.Biol. (2020)

Release Date

2020-02-05

Peptides

Integrase: ABEFIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
C

F
D

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Integrase

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