SMTL ID : 8eet.4 (4 other biounits)

T=1 particle HIV-1 CA M66A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 3 residues within 4Å: Chain A: R.18 Chain B: S.16 Ligands: IHP.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.13 Salt bridges: A:R.18 IHP.2: 8 residues within 4Å: Chain A: R.18, N.21, A.22, K.25 Chain B: R.18, A.22, K.25 Ligands: IHP.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.25, A:K.25, A:K.25, B:K.25, B:K.25 IHP.3: 4 residues within 4Å: Chain A: S.16, R.18 Chain B: R.18 Ligands: IHP.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.16, A:R.18 Salt bridges: A:R.18, B:R.18 IHP.4: 7 residues within 4Å: Chain A: A.22, K.25 Chain B: R.18, N.21, A.22, K.25 Ligands: IHP.2 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.25, A:K.25, B:K.25, B:K.25, B:K.25 Hydrogen bonds: B:R.18 IHP.5: 4 residues within 4Å: Chain C: R.18 Chain D: S.16, R.18 Ligands: IHP.7 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Salt bridges: C:R.18, D:R.18 Hydrogen bonds: D:S.16, D:R.18 IHP.6: 7 residues within 4Å: Chain C: R.18, N.21, A.22, K.25 Chain D: A.22, K.25 Ligands: IHP.8 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.18 Salt bridges: C:K.25, C:K.25, C:K.25, D:K.25, D:K.25 IHP.7: 3 residues within 4Å: Chain C: S.16 Chain D: R.18 Ligands: IHP.5 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.18 Hydrogen bonds: C:Q.13 IHP.8: 8 residues within 4Å: Chain C: R.18, A.22, K.25 Chain D: R.18, N.21, A.22, K.25 Ligands: IHP.6 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Salt bridges: C:K.25, C:K.25, D:K.25, D:K.25, D:K.25 IHP.9: 3 residues within 4Å: Chain E: R.18 Chain F: S.16 Ligands: IHP.11 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Salt bridges: E:R.18 Hydrogen bonds: F:Q.13 IHP.10: 8 residues within 4Å: Chain E: R.18, N.21, A.22, K.25 Chain F: R.18, A.22, K.25 Ligands: IHP.12 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Salt bridges: E:K.25, E:K.25, E:K.25, F:K.25, F:K.25 IHP.11: 4 residues within 4Å: Chain E: S.16, R.18 Chain F: R.18 Ligands: IHP.9 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Salt bridges: F:R.18, E:R.18 Hydrogen bonds: E:S.16, E:R.18 IHP.12: 7 residues within 4Å: Chain E: A.22, K.25 Chain F: R.18, N.21, A.22, K.25 Ligands: IHP.10 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.18 Salt bridges: F:K.25, F:K.25, F:K.25, E:K.25, E:K.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schirra, R.T. et al., A molecular switch modulates assembly and host factor binding of the HIV-1 capsid. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-02-15

Peptides

Gag polyprotein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Gag polyprotein

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