SMTL ID : 8f22.1 (1 other biounit)

HIV-CA Disulfide linked Hexamer bound to 11l capsid inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x XBQ: Nalpha-{[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]acetyl}-N-(4-methoxyphenyl)-N-methyl-L-phenylalaninamide(Non-covalent)

XBQ.1: 17 residues within 4Å: Chain A: N.53, L.56, N.57, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Chain F: Y.169, L.172, R.173, Q.176, T.186 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:L.56, A:L.69, A:K.70, A:I.73, A:A.105, A:T.107, A:T.107, F:L.172 Hydrogen bonds: A:N.57, A:N.57, F:Q.176 pi-Cation interactions: A:K.70 XBQ.2: 19 residues within 4Å: Chain A: Y.169, L.172, R.173, Q.176, A.184, A.185 Chain B: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.56, B:L.56, B:M.66, B:L.69, B:K.70, B:K.70, B:T.107, B:T.107, A:Y.169, A:Y.169, A:L.172 Hydrogen bonds: B:N.57, B:Q.63, B:K.70 pi-Cation interactions: B:K.70 XBQ.3: 18 residues within 4Å: Chain B: Y.169, L.172, R.173, Q.176, T.186 Chain C: N.53, L.56, N.57, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.56, C:M.66, C:L.69, C:K.70, C:I.73, C:T.107, C:T.107, B:Y.169, B:Y.169, B:T.186 Hydrogen bonds: C:N.57, C:N.57, B:R.173, B:T.186 Water bridges: C:Q.63 pi-Cation interactions: C:K.70 XBQ.4: 18 residues within 4Å: Chain C: Y.169, L.172, R.173, A.185 Chain D: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.56, D:L.56, D:M.66, D:L.69, D:K.70, D:A.105, D:T.107, D:T.107, C:Y.169, C:Y.169, C:L.172, C:A.185 Hydrogen bonds: D:N.57, D:N.57, D:Q.67, D:K.70 Water bridges: D:N.53, D:Q.63 pi-Cation interactions: D:K.70 XBQ.5: 18 residues within 4Å: Chain D: Y.169, L.172, R.173, Q.176 Chain E: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:L.56, E:L.56, E:M.66, E:L.69, E:K.70, E:A.105, E:T.107, E:T.107, D:Y.169, D:Y.169 Hydrogen bonds: E:N.57, E:N.57 pi-Cation interactions: E:K.70 XBQ.6: 17 residues within 4Å: Chain E: Y.169, L.172, R.173, Q.176, T.186 Chain F: N.53, L.56, N.57, M.66, Q.67, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:N.53, F:L.56, F:L.56, F:M.66, F:K.70, F:I.73, F:I.73, F:A.105, F:T.107, E:L.172, E:T.186 Hydrogen bonds: F:N.57, F:N.57, F:K.70 Water bridges: F:Q.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnett, M. et al., Structure of a benzosulfonamide based inhibitor - bound to a disulfide stabilised HIV-1 capsid hexamer. Biorxiv (2023)

Release Date

2023-09-13

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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