SMTL ID : 7zud.1

Crystal structure of HIV-1 capsid IP6-CPSF6 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

hetero-6-6-mer

Ligands

12 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)(Covalent)

IHP.1: 11 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.3, IHP.5, IHP.7, IHP.9, IHP.11 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain E, 1 interactions with chain G, 1 interactions with chain A, 1 interactions with chain C Salt bridges: K:R.18, G:R.18, A:R.18, C:R.18 Hydrogen bonds: E:R.18 IHP.2: 12 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: P.17, R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.4, IHP.6, IHP.8, IHP.10, IHP.12 13 PLIP interactions: 2 interactions with chain G, 2 interactions with chain I, 2 interactions with chain K, 3 interactions with chain E, 2 interactions with chain A, 2 interactions with chain C Salt bridges: G:R.18, G:R.18, I:R.18, I:R.18, K:R.18, K:R.18, E:R.18, E:R.18, E:R.18, A:R.18, A:R.18, C:R.18, C:R.18 IHP.3: 11 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.5, IHP.7, IHP.9, IHP.11 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 1 interactions with chain A, 1 interactions with chain I, 1 interactions with chain C Salt bridges: E:R.18, G:R.18, I:R.18, C:R.18 Hydrogen bonds: A:R.18 IHP.4: 12 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: P.17, R.18 Chain K: R.18 Ligands: IHP.2, IHP.6, IHP.8, IHP.10, IHP.12 13 PLIP interactions: 2 interactions with chain G, 2 interactions with chain I, 2 interactions with chain K, 2 interactions with chain E, 3 interactions with chain A, 2 interactions with chain C Salt bridges: G:R.18, G:R.18, I:R.18, I:R.18, K:R.18, K:R.18, E:R.18, E:R.18, A:R.18, A:R.18, A:R.18, C:R.18, C:R.18 IHP.5: 11 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.3, IHP.7, IHP.9, IHP.11 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain I, 1 interactions with chain C Salt bridges: K:R.18, E:R.18, A:R.18, I:R.18 Hydrogen bonds: C:R.18 IHP.6: 12 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: P.17, R.18 Ligands: IHP.2, IHP.4, IHP.8, IHP.10, IHP.12 13 PLIP interactions: 2 interactions with chain G, 2 interactions with chain I, 2 interactions with chain K, 2 interactions with chain E, 2 interactions with chain A, 3 interactions with chain C Salt bridges: G:R.18, G:R.18, I:R.18, I:R.18, K:R.18, K:R.18, E:R.18, E:R.18, A:R.18, A:R.18, C:R.18, C:R.18, C:R.18 IHP.7: 11 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.9, IHP.11 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain E, 1 interactions with chain G, 1 interactions with chain A, 1 interactions with chain I Hydrogen bonds: K:R.18 Salt bridges: E:R.18, G:R.18, A:R.18, I:R.18 IHP.8: 12 residues within 4Å: Chain A: P.17, R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.2, IHP.4, IHP.6, IHP.10, IHP.12 13 PLIP interactions: 2 interactions with chain G, 2 interactions with chain I, 3 interactions with chain K, 2 interactions with chain E, 2 interactions with chain A, 2 interactions with chain C Salt bridges: G:R.18, G:R.18, I:R.18, I:R.18, K:R.18, K:R.18, K:R.18, E:R.18, E:R.18, A:R.18, A:R.18, C:R.18, C:R.18 IHP.9: 11 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.7, IHP.11 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain G, 1 interactions with chain A, 1 interactions with chain I, 1 interactions with chain C Salt bridges: K:R.18, A:R.18, I:R.18, C:R.18 Hydrogen bonds: G:R.18 IHP.10: 12 residues within 4Å: Chain A: R.18 Chain C: P.17, R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.2, IHP.4, IHP.6, IHP.8, IHP.12 13 PLIP interactions: 3 interactions with chain G, 2 interactions with chain I, 2 interactions with chain K, 2 interactions with chain E, 2 interactions with chain A, 2 interactions with chain C Salt bridges: G:R.18, G:R.18, G:R.18, I:R.18, I:R.18, K:R.18, K:R.18, E:R.18, E:R.18, A:R.18, A:R.18, C:R.18, C:R.18 IHP.11: 11 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.7, IHP.9 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain E, 1 interactions with chain G, 1 interactions with chain I, 1 interactions with chain C Salt bridges: K:R.18, E:R.18, G:R.18, C:R.18 Hydrogen bonds: I:R.18 IHP.12: 12 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: P.17, R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.2, IHP.4, IHP.6, IHP.8, IHP.10 13 PLIP interactions: 2 interactions with chain G, 3 interactions with chain I, 2 interactions with chain K, 2 interactions with chain E, 2 interactions with chain A, 2 interactions with chain C Salt bridges: G:R.18, G:R.18, I:R.18, I:R.18, I:R.18, K:R.18, K:R.18, E:R.18, E:R.18, A:R.18, A:R.18, C:R.18, C:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicastro, G. et al., CP-MAS and Solution NMR Studies of Allosteric Communication in CA-assemblies of HIV-1. J.Mol.Biol. (2022)

Release Date

2022-07-27

Peptides

Capsid protein p24: ACEGIK
Cleavage and polyadenylation specificity factor subunit 6: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

B
M

D
M

F
M

H
M

J
M

L
M

Capsid protein p24

Cleavage and polyadenylation specificity factor subunit 6