SMTL ID : 9clj.3 (4 other biounits)

HIV-2 CA T=1 Icosahedron; assembled via lipid templating

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

IHP.1: 12 residues within 4Å: Chain A: S.16, R.18 Chain B: S.16 Chain C: S.16, T.19 Chain D: S.16, R.18 Chain E: S.16 Ligands: IHP.3, IHP.5, IHP.7, IHP.9 12 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D, 3 interactions with chain A, 2 interactions with chain C, 2 interactions with chain E Hydrogen bonds: B:S.16, B:R.18, D:S.16, A:S.16, C:S.16, C:T.19, E:S.16, E:R.18 Water bridges: D:T.19, A:R.18 Salt bridges: D:R.18, A:R.18 IHP.2: 20 residues within 4Å: Chain A: R.18, A.22, K.25 Chain B: R.18, A.22, K.25 Chain C: R.18, A.22, K.25 Chain D: R.18, A.22, K.25 Chain E: R.18, N.21, A.22, K.25 Ligands: IHP.4, IHP.6, IHP.8, IHP.10 32 PLIP interactions: 8 interactions with chain D, 6 interactions with chain C, 6 interactions with chain B, 7 interactions with chain E, 5 interactions with chain A Hydrogen bonds: D:R.18, B:R.18, E:N.21, A:R.18 Water bridges: D:N.21, D:N.21, D:K.25, C:K.25, C:K.25, B:N.21, B:N.21, E:K.25, E:K.25, A:K.25 Salt bridges: D:R.18, D:K.25, D:K.25, D:K.25, C:R.18, C:K.25, C:K.25, C:K.25, B:R.18, B:K.25, B:K.25, E:R.18, E:K.25, E:K.25, E:K.25, A:R.18, A:K.25, A:K.25 IHP.3: 12 residues within 4Å: Chain A: S.16 Chain B: S.16, R.18 Chain C: S.16 Chain D: S.16, T.19 Chain E: S.16, R.18 Ligands: IHP.1, IHP.5, IHP.7, IHP.9 11 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: B:S.16, A:S.16, A:R.18, C:S.16, C:R.18, E:S.16, D:S.16, D:T.19 Water bridges: B:R.18 Salt bridges: B:R.18, E:R.18 IHP.4: 20 residues within 4Å: Chain A: R.18, N.21, A.22, K.25 Chain B: R.18, A.22, K.25 Chain C: R.18, A.22, K.25 Chain D: R.18, A.22, K.25 Chain E: R.18, A.22, K.25 Ligands: IHP.2, IHP.6, IHP.8, IHP.10 32 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D, 8 interactions with chain E, 5 interactions with chain B, 7 interactions with chain A Hydrogen bonds: C:R.18, E:R.18, B:R.18, A:N.21 Water bridges: C:N.21, C:N.21, D:K.25, D:K.25, E:N.21, E:N.21, E:K.25, B:K.25, A:K.25, A:K.25 Salt bridges: C:R.18, C:K.25, C:K.25, D:R.18, D:K.25, D:K.25, D:K.25, E:R.18, E:K.25, E:K.25, E:K.25, B:R.18, B:K.25, B:K.25, A:R.18, A:K.25, A:K.25, A:K.25 IHP.5: 12 residues within 4Å: Chain A: S.16, R.18 Chain B: S.16 Chain C: S.16, R.18 Chain D: S.16 Chain E: S.16, T.19 Ligands: IHP.1, IHP.3, IHP.7, IHP.9 11 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 interactions with chain E, 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:S.16, B:R.18, D:S.16, D:R.18, E:S.16, E:T.19, A:S.16, C:S.16 Salt bridges: A:R.18, C:R.18 Water bridges: C:R.18 IHP.6: 20 residues within 4Å: Chain A: R.18, A.22, K.25 Chain B: R.18, N.21, A.22, K.25 Chain C: R.18, A.22, K.25 Chain D: R.18, A.22, K.25 Chain E: R.18, A.22, K.25 Ligands: IHP.2, IHP.4, IHP.8, IHP.10 32 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C, 7 interactions with chain B, 6 interactions with chain E, 8 interactions with chain A Hydrogen bonds: D:R.18, C:R.18, B:N.21, A:R.18 Water bridges: D:N.21, D:N.21, C:K.25, B:K.25, B:K.25, E:K.25, E:K.25, A:N.21, A:N.21, A:K.25 Salt bridges: D:R.18, D:K.25, D:K.25, C:R.18, C:K.25, C:K.25, B:R.18, B:K.25, B:K.25, B: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 IHP.7: 12 residues within 4Å: Chain A: S.16, T.19 Chain B: S.16, R.18 Chain C: S.16 Chain D: S.16, R.18 Chain E: S.16 Ligands: IHP.1, IHP.3, IHP.5, IHP.9 12 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D, 2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain E Hydrogen bonds: B:S.16, D:S.16, A:S.16, A:T.19, C:S.16, C:R.18, E:S.16, E:R.18 Water bridges: B:T.19, D:R.18 Salt bridges: B:R.18, D:R.18 IHP.8: 20 residues within 4Å: Chain A: R.18, A.22, K.25 Chain B: R.18, A.22, K.25 Chain C: R.18, N.21, A.22, K.25 Chain D: R.18, A.22, K.25 Chain E: R.18, A.22, K.25 Ligands: IHP.2, IHP.4, IHP.6, IHP.10 32 PLIP interactions: 7 interactions with chain C, 5 interactions with chain D, 8 interactions with chain B, 6 interactions with chain E, 6 interactions with chain A Hydrogen bonds: C:N.21, D:R.18, B:R.18, E:R.18 Water bridges: C:K.25, C:K.25, D:K.25, B:N.21, B:N.21, B:K.25, E:N.21, E:N.21, A:K.25, A:K.25 Salt bridges: C:R.18, C:K.25, C:K.25, C:K.25, D:R.18, D:K.25, D:K.25, B:R.18, B:K.25, B:K.25, B:K.25, E:R.18, E:K.25, E:K.25, A:R.18, A:K.25, A:K.25, A:K.25 IHP.9: 12 residues within 4Å: Chain A: S.16 Chain B: S.16, T.19 Chain C: S.16, R.18 Chain D: S.16 Chain E: S.16, R.18 Ligands: IHP.1, IHP.3, IHP.5, IHP.7 12 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 interactions with chain A, 3 interactions with chain C, 3 interactions with chain E Hydrogen bonds: B:S.16, B:T.19, D:S.16, D:R.18, A:S.16, A:R.18, C:S.16, E:S.16 Water bridges: C:T.19, E:R.18 Salt bridges: C:R.18, E:R.18 IHP.10: 20 residues within 4Å: Chain A: R.18, A.22, K.25 Chain B: R.18, A.22, K.25 Chain C: R.18, A.22, K.25 Chain D: R.18, N.21, A.22, K.25 Chain E: R.18, A.22, K.25 Ligands: IHP.2, IHP.4, IHP.6, IHP.8 32 PLIP interactions: 8 interactions with chain C, 7 interactions with chain D, 5 interactions with chain E, 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: C:R.18, D:N.21, E:R.18, A:R.18 Water bridges: C:N.21, C:N.21, C:K.25, D:K.25, D:K.25, E:K.25, B:K.25, B:K.25, A:N.21, A:N.21 Salt bridges: C:R.18, C:K.25, C:K.25, C:K.25, D:R.18, D:K.25, D:K.25, D:K.25, E:R.18, E:K.25, E:K.25, B:R.18, B:K.25, B:K.25, B:K.25, A:R.18, A:K.25, A:K.25

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: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

Capsid protein p24

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