SMTL ID : 9cns.1 (1 other biounit)

HIV-2 CA hexamer; assembled via liposome templating

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

12 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 11 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.3, IHP.5, IHP.7, IHP.9, IHP.11 11 PLIP interactions: 1 interactions with chain D, 2 interactions with chain P, 2 interactions with chain A, 2 interactions with chain G, 1 interactions with chain J, 3 interactions with chain M Hydrogen bonds: D:R.18, P:R.18, A:R.18, A:R.18, G:R.18, M:R.18, M:R.18 Salt bridges: P:R.18, G:R.18, J:R.18, M:R.18 IHP.2: 10 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Ligands: IHP.4, IHP.6, IHP.8, IHP.10, IHP.12 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 2 interactions with chain G, 1 interactions with chain J, 1 interactions with chain M Salt bridges: D:R.18, A:R.18, G:R.18, G:R.18, J:R.18, M:R.18 IHP.3: 11 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.1, IHP.5, IHP.7, IHP.9, IHP.11 11 PLIP interactions: 2 interactions with chain D, 3 interactions with chain P, 2 interactions with chain A, 1 interactions with chain G, 2 interactions with chain J, 1 interactions with chain M Hydrogen bonds: D:R.18, D:R.18, P:R.18, P:R.18, A:R.18, G:R.18, J:R.18 Salt bridges: P:R.18, A:R.18, J:R.18, M:R.18 IHP.4: 10 residues within 4Å: Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.2, IHP.6, IHP.8, IHP.10, IHP.12 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain P, 1 interactions with chain G, 2 interactions with chain J, 1 interactions with chain M Salt bridges: D:R.18, P:R.18, G:R.18, J:R.18, J:R.18, M:R.18 IHP.5: 11 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.1, IHP.3, IHP.7, IHP.9, IHP.11 11 PLIP interactions: 2 interactions with chain D, 1 interactions with chain P, 3 interactions with chain A, 2 interactions with chain M, 2 interactions with chain G, 1 interactions with chain J Hydrogen bonds: D:R.18, A:R.18, A:R.18, M:R.18, G:R.18, G:R.18, J:R.18 Salt bridges: D:R.18, P:R.18, A:R.18, M:R.18 IHP.6: 10 residues within 4Å: Chain A: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.2, IHP.4, IHP.8, IHP.10, IHP.12 6 PLIP interactions: 1 interactions with chain P, 1 interactions with chain A, 1 interactions with chain G, 1 interactions with chain J, 2 interactions with chain M Salt bridges: P:R.18, A:R.18, G:R.18, J:R.18, M:R.18, M:R.18 IHP.7: 11 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.9, IHP.11 11 PLIP interactions: 3 interactions with chain D, 2 interactions with chain P, 1 interactions with chain A, 1 interactions with chain M, 2 interactions with chain G, 2 interactions with chain J Hydrogen bonds: D:R.18, D:R.18, P:R.18, M:R.18, G:R.18, J:R.18, J:R.18 Salt bridges: D:R.18, P:R.18, A:R.18, G:R.18 IHP.8: 10 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.2, IHP.4, IHP.6, IHP.10, IHP.12 6 PLIP interactions: 1 interactions with chain D, 2 interactions with chain P, 1 interactions with chain A, 1 interactions with chain J, 1 interactions with chain M Salt bridges: D:R.18, P:R.18, P:R.18, A:R.18, J:R.18, M:R.18 IHP.9: 11 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.7, IHP.11 11 PLIP interactions: 1 interactions with chain D, 1 interactions with chain P, 2 interactions with chain A, 2 interactions with chain M, 3 interactions with chain G, 2 interactions with chain J Salt bridges: D:R.18, A:R.18, G:R.18, J:R.18 Hydrogen bonds: P:R.18, A:R.18, M:R.18, M:R.18, G:R.18, G:R.18, J:R.18 IHP.10: 10 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.2, IHP.4, IHP.6, IHP.8, IHP.12 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain P, 2 interactions with chain A, 1 interactions with chain G, 1 interactions with chain M Salt bridges: D:R.18, P:R.18, A:R.18, A:R.18, G:R.18, M:R.18 IHP.11: 11 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain M: R.18 Chain P: R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.7, IHP.9 11 PLIP interactions: 2 interactions with chain D, 2 interactions with chain P, 1 interactions with chain A, 2 interactions with chain M, 1 interactions with chain G, 3 interactions with chain J Hydrogen bonds: D:R.18, P:R.18, P:R.18, A:R.18, M:R.18, J:R.18, J:R.18 Salt bridges: D:R.18, M:R.18, G:R.18, J:R.18 IHP.12: 10 residues within 4Å: Chain A: R.18 Chain D: R.18 Chain G: R.18 Chain J: R.18 Chain P: R.18 Ligands: IHP.2, IHP.4, IHP.6, IHP.8, IHP.10 6 PLIP interactions: 2 interactions with chain D, 1 interactions with chain P, 1 interactions with chain A, 1 interactions with chain G, 1 interactions with chain J Salt bridges: D:R.18, D:R.18, P:R.18, A:R.18, G:R.18, J:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, M. et al., Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single-particle cryo-EM. Cell Rep (2025)

Release Date

2025-03-05

Peptides

Capsid protein p24: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

P
A

Q
B

R
C

Capsid protein p24

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