SMTL ID : 4obf.1 (1 other biounit)

Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease Variant (D30N/N88D) in Complex with the p1-p6 substrate variant (S451N)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

hetero-2-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: K.7, R.8 Chain B: R.87 Chain C: R.9 Ligands: EDO.4 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:R.8, B:R.87, B:R.87, C:R.9, C:R.9 Water bridges: A:R.8 GOL.7: 3 residues within 4Å: Chain A: R.87 Chain B: K.7, R.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.87, A:R.87, B:R.8

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: R.14, I.15, G.16, G.17, P.63, I.64, E.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.17, A:P.63, A:E.65 EDO.3: 3 residues within 4Å: Chain A: G.68, H.69, K.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.70 EDO.4: 6 residues within 4Å: Chain A: L.5, W.6 Chain B: R.87, T.91 Chain C: R.9 Ligands: GOL.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.87, B:R.87, B:T.91, C:R.9 EDO.8: 7 residues within 4Å: Chain B: R.14, I.15, G.16, G.17, P.63, I.64, E.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.17 Water bridges: B:I.64, B:I.64 EDO.9: 4 residues within 4Å: Chain A: R.8 Chain C: N.8, R.9, P.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.8, A:R.8, C:P.10 Water bridges: C:N.8

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 3 residues within 4Å: Chain A: E.35, M.36, N.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:N.37

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 1 residues within 4Å: Chain A: P.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolli, M. et al., HIV-1 protease-substrate coevolution in nelfinavir resistance. J.Virol. (2014)

Release Date

2014-11-26

Peptides

HIV-1 Protease: AB
p1-p6 peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

HIV-1 Protease

p1-p6 peptide

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