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

HIV-2 CA pentamer; assembled via liposome templating

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-20-mer

Ligands

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

IHP.1: 13 residues within 4Å: Chain A: S.16, R.18 Chain E: S.16, R.18 Chain I: S.16, R.18 Chain M: S.16, R.18 Chain Q: R.18 Ligands: IHP.3, IHP.5, IHP.7, IHP.9 9 PLIP interactions: 2 interactions with chain M, 2 interactions with chain I, 1 interactions with chain Q, 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: M:S.16, I:S.16, E:S.16, A:S.16 Salt bridges: M:R.18, I:R.18, Q:R.18, E:R.18, A:R.18 IHP.2: 17 residues within 4Å: Chain A: R.18, K.25 Chain E: R.18, A.22, K.25 Chain I: R.18, A.22, K.25 Chain M: R.18, K.25 Chain Q: R.18, A.22, K.25 Ligands: IHP.4, IHP.6, IHP.8, IHP.10 20 PLIP interactions: 5 interactions with chain M, 4 interactions with chain I, 4 interactions with chain E, 4 interactions with chain A, 3 interactions with chain Q Hydrogen bonds: M:R.18, A:R.18 Salt bridges: M:R.18, M:K.25, M:K.25, M:K.25, I:R.18, I:K.25, I:K.25, I:K.25, E:R.18, E:K.25, E:K.25, E:K.25, A:R.18, A:K.25, A:K.25, Q:R.18, Q:K.25, Q:K.25 IHP.3: 13 residues within 4Å: Chain A: R.18 Chain E: S.16, R.18 Chain I: S.16, R.18 Chain M: S.16, R.18 Chain Q: S.16, R.18 Ligands: IHP.1, IHP.5, IHP.7, IHP.9 9 PLIP interactions: 2 interactions with chain M, 2 interactions with chain I, 2 interactions with chain Q, 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: M:S.16, I:S.16, Q:S.16, E:S.16 Salt bridges: M:R.18, I:R.18, Q:R.18, E:R.18, A:R.18 IHP.4: 17 residues within 4Å: Chain A: R.18, A.22, K.25 Chain E: R.18, K.25 Chain I: R.18, A.22, K.25 Chain M: R.18, A.22, K.25 Chain Q: R.18, K.25 Ligands: IHP.2, IHP.6, IHP.8, IHP.10 20 PLIP interactions: 4 interactions with chain M, 4 interactions with chain I, 4 interactions with chain E, 3 interactions with chain A, 5 interactions with chain Q Salt bridges: M:R.18, M:K.25, M:K.25, M:K.25, I:R.18, I:K.25, I:K.25, I:K.25, E:R.18, E:K.25, E:K.25, A:R.18, A:K.25, A:K.25, Q:R.18, Q:R.18, Q:K.25, Q:K.25, Q:K.25 Hydrogen bonds: E:R.18 IHP.5: 13 residues within 4Å: Chain A: S.16, R.18 Chain E: R.18 Chain I: S.16, R.18 Chain M: S.16, R.18 Chain Q: S.16, R.18 Ligands: IHP.1, IHP.3, IHP.7, IHP.9 9 PLIP interactions: 2 interactions with chain M, 2 interactions with chain I, 2 interactions with chain Q, 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: M:S.16, I:S.16, Q:S.16, A:S.16 Salt bridges: M:R.18, I:R.18, Q:R.18, E:R.18, A:R.18 IHP.6: 17 residues within 4Å: Chain A: R.18, K.25 Chain E: R.18, A.22, K.25 Chain I: R.18, K.25 Chain M: R.18, A.22, K.25 Chain Q: R.18, A.22, K.25 Ligands: IHP.2, IHP.4, IHP.8, IHP.10 20 PLIP interactions: 4 interactions with chain M, 4 interactions with chain I, 3 interactions with chain E, 5 interactions with chain A, 4 interactions with chain Q Salt bridges: M:R.18, M:K.25, M:K.25, M:K.25, I:R.18, I:K.25, I:K.25, E:R.18, E:K.25, E:K.25, A:R.18, A:R.18, A:K.25, A:K.25, A:K.25, Q:R.18, Q:K.25, Q:K.25, Q:K.25 Hydrogen bonds: I:R.18 IHP.7: 13 residues within 4Å: Chain A: S.16, R.18 Chain E: S.16, R.18 Chain I: R.18 Chain M: S.16, R.18 Chain Q: S.16, R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.9 9 PLIP interactions: 2 interactions with chain M, 1 interactions with chain I, 2 interactions with chain Q, 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: M:S.16, Q:S.16, E:S.16, A:S.16 Salt bridges: M:R.18, I:R.18, Q:R.18, E:R.18, A:R.18 IHP.8: 17 residues within 4Å: Chain A: R.18, A.22, K.25 Chain E: R.18, K.25 Chain I: R.18, A.22, K.25 Chain M: R.18, K.25 Chain Q: R.18, A.22, K.25 Ligands: IHP.2, IHP.4, IHP.6, IHP.10 20 PLIP interactions: 4 interactions with chain M, 3 interactions with chain I, 5 interactions with chain E, 4 interactions with chain A, 4 interactions with chain Q Hydrogen bonds: M:R.18, E:R.18 Salt bridges: M:R.18, M:K.25, M:K.25, I:R.18, I:K.25, I:K.25, E:R.18, E:K.25, E:K.25, E:K.25, A:R.18, A:K.25, A:K.25, A:K.25, Q:R.18, Q:K.25, Q:K.25, Q:K.25 IHP.9: 13 residues within 4Å: Chain A: S.16, R.18 Chain E: S.16, R.18 Chain I: S.16, R.18 Chain M: R.18 Chain Q: S.16, R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.7 9 PLIP interactions: 2 interactions with chain I, 2 interactions with chain Q, 1 interactions with chain M, 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: I:S.16, Q:S.16, E:S.16, A:S.16 Salt bridges: I:R.18, Q:R.18, M:R.18, E:R.18, A:R.18 IHP.10: 17 residues within 4Å: Chain A: R.18, A.22, K.25 Chain E: R.18, A.22, K.25 Chain I: R.18, K.25 Chain M: R.18, A.22, K.25 Chain Q: R.18, K.25 Ligands: IHP.2, IHP.4, IHP.6, IHP.8 19 PLIP interactions: 2 interactions with chain M, 5 interactions with chain I, 4 interactions with chain E, 4 interactions with chain A, 4 interactions with chain Q Salt bridges: M:R.18, M:K.25, I:R.18, I:R.18, I:K.25, I:K.25, I:K.25, E:R.18, E:K.25, E:K.25, E:K.25, A:R.18, A:K.25, A:K.25, A:K.25, Q:R.18, Q:K.25, Q:K.25 Hydrogen bonds: Q: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: ABCDEFGHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

M
A

N
B

O
C

P
D

Q
A

R
B

S
C

T
D

Capsid protein p24

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