SMTL ID : 5hgl.1

Hexameric HIV-1 CA, open conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-hexamer

Ligands

6 x 1B0: N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE(Non-covalent)

1B0.1: 12 residues within 4Å: Chain A: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, A.105, T.107, Y.130 Chain F: R.173 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:L.56, A:L.56, A:M.66, A:L.69, A:K.70, A:I.73, A:I.73, A:T.107, F:R.173 Hydrogen bonds: A:N.57, A:N.57, A:Q.63, A:K.70 pi-Cation interactions: A:K.70, A:K.70 1B0.2: 16 residues within 4Å: Chain A: R.173, Q.176, S.178, Q.179, E.180 Chain B: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, A.105, T.107, Y.130 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:R.173, B:L.56, B:L.56, B:M.66, B:L.69, B:I.73, B:I.73 Hydrogen bonds: A:E.180, B:N.57, B:N.57, B:Q.63, B:K.70 pi-Cation interactions: B:K.70, B:K.70 1B0.4: 13 residues within 4Å: Chain B: Y.169, R.173 Chain C: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, A.105, T.107, Y.130 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.56, C:L.56, C:M.66, C:L.69, C:K.70, C:I.73, C:I.73, C:T.107, C:T.107, B:R.173, B:R.173 Hydrogen bonds: C:N.57, C:N.57, C:Q.63, C:K.70 pi-Cation interactions: C:K.70, C:K.70 1B0.5: 11 residues within 4Å: Chain C: R.173 Chain D: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, T.107, Y.130 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.56, D:L.56, D:M.66, D:L.69, D:K.70, D:I.73, D:I.73, D:T.107, C:R.173 Hydrogen bonds: D:N.57, D:N.57, D:Q.63, D:K.70 pi-Cation interactions: D:K.70, D:K.70 1B0.6: 12 residues within 4Å: Chain D: R.173 Chain E: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, A.105, T.107, Y.130 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:L.56, E:L.56, E:L.69, E:K.70, E:I.73, E:I.73, E:T.107 Hydrogen bonds: E:N.57, E:N.57, E:Q.63, E:K.70 pi-Cation interactions: E:K.70, E:K.70 1B0.7: 13 residues within 4Å: Chain E: Y.169, R.173 Chain F: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, A.105, T.107, Y.130 14 PLIP interactions: 2 interactions with chain E, 12 interactions with chain F Hydrophobic interactions: E:R.173, E:R.173, F:L.56, F:M.66, F:L.69, F:K.70, F:I.73, F:I.73 Hydrogen bonds: F:N.57, F:N.57, F:Q.63, F:K.70 pi-Cation interactions: F:K.70, F:K.70

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: R.18 Chain B: R.18 Chain E: R.18 Chain F: R.18 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacques, D.A. et al., HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis. Nature (2016)

Release Date

2016-08-10

Peptides

Capsid protein P24: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Capsid protein P24

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