SMTL ID : 6bhr.1

HIV-1 immature CTD-SP1 hexamer in complex with IP6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

homo-hexamer

Ligands

6 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 16 residues within 4Å: Chain A: K.13, K.82 Chain B: K.13, K.82 Chain C: K.13, K.82 Chain D: K.13, K.82 Chain E: K.82 Chain F: K.13, K.82 Ligands: IHP.2, IHP.3, IHP.4, IHP.5, IHP.6 19 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C, 3 interactions with chain A, 4 interactions with chain F, 3 interactions with chain B, 2 interactions with chain E Salt bridges: D:K.13, D:K.82, D:K.82, C:K.13, C:K.82, C:K.82, C:K.82, A:K.13, A:K.82, A:K.82, F:K.13, F:K.82, F:K.82, F:K.82, B:K.13, B:K.82, B:K.82, E:K.82, E:K.82 IHP.2: 16 residues within 4Å: Chain A: K.13, K.82 Chain B: K.13, K.82 Chain C: K.13, K.82 Chain D: K.13, K.82 Chain E: K.13, K.82 Chain F: K.82 Ligands: IHP.1, IHP.3, IHP.4, IHP.5, IHP.6 19 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C, 4 interactions with chain A, 3 interactions with chain E, 2 interactions with chain F, 3 interactions with chain B Salt bridges: D:K.13, D:K.82, D:K.82, D:K.82, C:K.13, C:K.82, C:K.82, A:K.13, A:K.82, A:K.82, A:K.82, E:K.13, E:K.82, E:K.82, F:K.82, F:K.82, B:K.13, B:K.82, B:K.82 IHP.3: 16 residues within 4Å: Chain A: K.13, K.82 Chain B: K.13, K.82 Chain C: K.13, K.82 Chain D: K.82 Chain E: K.13, K.82 Chain F: K.13, K.82 Ligands: IHP.1, IHP.2, IHP.4, IHP.5, IHP.6 19 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C, 3 interactions with chain A, 4 interactions with chain E, 3 interactions with chain F, 4 interactions with chain B Salt bridges: D:K.82, D:K.82, C:K.13, C:K.82, C:K.82, A:K.13, A:K.82, A:K.82, E:K.13, E:K.82, E:K.82, E:K.82, F:K.13, F:K.82, F:K.82, B:K.13, B:K.82, B:K.82, B:K.82 IHP.4: 16 residues within 4Å: Chain A: K.13, K.82 Chain B: K.82 Chain C: K.13, K.82 Chain D: K.13, K.82 Chain E: K.13, K.82 Chain F: K.13, K.82 Ligands: IHP.1, IHP.2, IHP.3, IHP.5, IHP.6 19 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C, 3 interactions with chain A, 3 interactions with chain E, 4 interactions with chain F, 2 interactions with chain B Salt bridges: D:K.13, D:K.82, D:K.82, C:K.13, C:K.82, C:K.82, C:K.82, A:K.13, A:K.82, A:K.82, E:K.13, E:K.82, E:K.82, F:K.13, F:K.82, F:K.82, F:K.82, B:K.82, B:K.82 IHP.5: 16 residues within 4Å: Chain A: K.13, K.82 Chain B: K.13, K.82 Chain C: K.82 Chain D: K.13, K.82 Chain E: K.13, K.82 Chain F: K.13, K.82 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.6 19 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A, 3 interactions with chain E, 3 interactions with chain F, 3 interactions with chain B, 2 interactions with chain C Salt bridges: D:K.13, D:K.82, D:K.82, D:K.82, A:K.13, A:K.82, A:K.82, A:K.82, E:K.13, E:K.82, E:K.82, F:K.13, F:K.82, F:K.82, B:K.13, B:K.82, B:K.82, C:K.82, C:K.82 IHP.6: 16 residues within 4Å: Chain A: K.82 Chain B: K.13, K.82 Chain C: K.13, K.82 Chain D: K.13, K.82 Chain E: K.13, K.82 Chain F: K.13, K.82 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5 19 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C, 2 interactions with chain A, 4 interactions with chain E, 3 interactions with chain F, 4 interactions with chain B Salt bridges: D:K.13, D:K.82, D:K.82, C:K.13, C:K.82, C:K.82, A:K.82, A:K.82, E:K.13, E:K.82, E:K.82, E:K.82, F:K.13, F:K.82, F:K.82, B:K.13, B:K.82, B:K.82, B:K.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dick, R.A. et al., Inositol phosphates are assembly co-factors for HIV-1. Nature (2018)

Release Date

2018-08-08

Peptides

Capsid protein p24,Spacer peptide 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
G

C
G

D
G

E
G

F
G

Capsid protein p24,Spacer peptide 1