SMTL ID : 6r8c.1

HIV capsid hexamer with IP5 ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-hexamer

Ligands

6 x 5MY: MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE(Non-covalent)

5MY.1: 12 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain C: R.18 Chain D: R.18 Chain E: R.18 Chain F: S.16, R.18 Ligands: 5MY.2, 5MY.3, 5MY.4, 5MY.5, 5MY.6 12 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E, 3 interactions with chain A, 1 interactions with chain C, 3 interactions with chain F, 2 interactions with chain D Salt bridges: B:R.18, B:R.18, E:R.18, A:R.18, A:R.18, C:R.18, F:R.18, F:R.18, D:R.18, D:R.18 Hydrogen bonds: A:R.18, F:S.16 5MY.2: 12 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain C: R.18 Chain D: S.16, R.18 Chain E: R.18 Chain F: R.18 Ligands: 5MY.1, 5MY.3, 5MY.4, 5MY.5, 5MY.6 12 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E, 1 interactions with chain A, 2 interactions with chain C, 3 interactions with chain D, 1 interactions with chain F Hydrogen bonds: B:R.18, D:S.16 Salt bridges: B:R.18, B:R.18, E:R.18, E:R.18, A:R.18, C:R.18, C:R.18, D:R.18, D:R.18, F:R.18 5MY.3: 12 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain C: R.18 Chain D: R.18 Chain E: S.16, R.18 Chain F: R.18 Ligands: 5MY.1, 5MY.2, 5MY.4, 5MY.5, 5MY.6 12 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E, 2 interactions with chain A, 3 interactions with chain C, 2 interactions with chain F, 1 interactions with chain D Salt bridges: B:R.18, E:R.18, E:R.18, A:R.18, A:R.18, C:R.18, C:R.18, F:R.18, F:R.18, D:R.18 Hydrogen bonds: E:S.16, C:R.18 5MY.4: 12 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain C: S.16, R.18 Chain D: R.18 Chain E: R.18 Chain F: R.18 Ligands: 5MY.1, 5MY.2, 5MY.3, 5MY.5, 5MY.6 12 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 2 interactions with chain E, 2 interactions with chain A, 1 interactions with chain F, 3 interactions with chain D Hydrogen bonds: C:S.16, D:R.18 Salt bridges: C:R.18, C:R.18, B:R.18, E:R.18, E:R.18, A:R.18, A:R.18, F:R.18, D:R.18, D:R.18 5MY.5: 12 residues within 4Å: Chain A: S.16, R.18 Chain B: R.18 Chain C: R.18 Chain D: R.18 Chain E: R.18 Chain F: R.18 Ligands: 5MY.1, 5MY.2, 5MY.3, 5MY.4, 5MY.6 12 PLIP interactions: 2 interactions with chain B, 3 interactions with chain E, 3 interactions with chain A, 1 interactions with chain C, 2 interactions with chain F, 1 interactions with chain D Salt bridges: B:R.18, B:R.18, E:R.18, E:R.18, A:R.18, A:R.18, C:R.18, F:R.18, F:R.18, D:R.18 Hydrogen bonds: E:R.18, A:S.16 5MY.6: 12 residues within 4Å: Chain A: R.18 Chain B: S.16, R.18 Chain C: R.18 Chain D: R.18 Chain E: R.18 Chain F: R.18 Ligands: 5MY.1, 5MY.2, 5MY.3, 5MY.4, 5MY.5 12 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E, 1 interactions with chain A, 2 interactions with chain C, 3 interactions with chain F, 2 interactions with chain D Hydrogen bonds: B:S.16, F:R.18 Salt bridges: B:R.18, B:R.18, E:R.18, A:R.18, C:R.18, C:R.18, F:R.18, F:R.18, D:R.18, D:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

James, L.C., HIV hexamer. to be published

Release Date

2020-05-06

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