SMTL ID : 6h09.1

HIV capsid hexamer with IP6 ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x IHP: INOSITOL HEXAKISPHOSPHATE(Covalent)

IHP.1: 10 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain C: R.18 Chain E: R.18 Chain F: R.18 Ligands: IHP.2, IHP.3, IHP.4, IHP.5, IHP.6 13 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 3 interactions with chain E, 4 interactions with chain F, 1 interactions with chain A Hydrogen bonds: B:R.18, C:R.18 Water bridges: B:R.18, E:R.18, F:R.18, F:R.18 Salt bridges: B:R.18, C:R.18, E:R.18, E:R.18, F:R.18, F:R.18, A:R.18 IHP.2: 10 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain C: R.18 Chain D: R.18 Chain F: R.18 Ligands: IHP.1, IHP.3, IHP.4, IHP.5, IHP.6 13 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 4 interactions with chain D, 3 interactions with chain F, 2 interactions with chain A Salt bridges: B:R.18, C:R.18, D:R.18, D:R.18, F:R.18, F:R.18, A:R.18 Hydrogen bonds: C:R.18, A:R.18 Water bridges: C:R.18, D:R.18, D:R.18, F:R.18 IHP.3: 10 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain C: R.18 Chain D: R.18 Chain E: R.18 Ligands: IHP.1, IHP.2, IHP.4, IHP.5, IHP.6 13 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 4 interactions with chain E, 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: B:R.18, A:R.18 Salt bridges: B:R.18, C:R.18, E:R.18, E:R.18, D:R.18, D:R.18, A:R.18 Water bridges: E:R.18, E:R.18, D:R.18, A:R.18 IHP.4: 10 residues within 4Å: Chain B: R.18 Chain C: R.18 Chain D: R.18 Chain E: R.18 Chain F: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.5, IHP.6 13 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C, 3 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F Water bridges: B:R.18, C:R.18, C:R.18, E:R.18 Salt bridges: B:R.18, B:R.18, C:R.18, C:R.18, E:R.18, D:R.18, F:R.18 Hydrogen bonds: C:R.18, E:R.18 IHP.5: 10 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain D: R.18 Chain E: R.18 Chain F: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.6 13 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E, 1 interactions with chain D, 3 interactions with chain F, 5 interactions with chain A Water bridges: C:R.18, F:R.18, A:R.18, A:R.18 Salt bridges: C:R.18, C:R.18, E:R.18, D:R.18, F:R.18, A:R.18, A:R.18 Hydrogen bonds: F:R.18, A:R.18 IHP.6: 10 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain D: R.18 Chain E: R.18 Chain F: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5 13 PLIP interactions: 5 interactions with chain B, 1 interactions with chain E, 3 interactions with chain D, 1 interactions with chain F, 3 interactions with chain A Hydrogen bonds: B:R.18, D:R.18 Water bridges: B:R.18, B:R.18, D:R.18, A:R.18 Salt bridges: B:R.18, B:R.18, E:R.18, D:R.18, F:R.18, A:R.18, A:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mallery, D.L. et al., IP6 is an HIV pocket factor that prevents capsid collapse and promotes DNA synthesis. Elife (2018)

Release Date

2018-08-15

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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