SMTL ID : 3lzv.1

Structure of Nelfinavir-resistant HIV-1 protease (D30N/N88D) in complex with Darunavir.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

1 x 017: (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE(Non-covalent)

017.1: 24 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, N.30, I.47, G.48, G.49, I.50, V.82 Chain B: R.8, D.25, G.27, A.28, N.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84 20 PLIP interactions: 11 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:L.23, A:I.50, A:V.82, B:A.28, B:V.32, B:P.81, B:V.82, B:I.84 Hydrogen bonds: A:D.25, A:G.27, A:G.27, A:D.29, A:N.30, A:N.30, B:N.30, B:N.30 Water bridges: A:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

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

PO4.2: 3 residues within 4Å: Chain A: R.14, G.16, G.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:G.17 Salt bridges: A:R.14 PO4.3: 3 residues within 4Å: Chain A: K.20, E.21, N.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.21 Water bridges: A:K.20, A:E.34 PO4.4: 4 residues within 4Å: Chain A: Q.18, E.35, M.36, N.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.18, A:N.37, A:N.37 PO4.5: 4 residues within 4Å: Chain A: R.87 Chain B: W.6, K.7, R.8 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.8, B:R.8 Water bridges: A:R.87, A:R.87 Salt bridges: A:R.87 PO4.8: 5 residues within 4Å: Chain B: L.19, K.20, E.21, E.34, N.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.19, B:E.21, B:N.83

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

ACT.6: 1 residues within 4Å: Chain A: R.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.8 Hydrogen bonds: A:R.8 ACT.7: 2 residues within 4Å: Chain A: P.44, K.45 3 PLIP interactions: 3 interactions with chain A Water bridges: A:M.46, A:M.46 Salt bridges: A:K.45 ACT.9: 3 residues within 4Å: Chain B: K.43, K.45, Q.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.58 Salt bridges: B:K.43, B:K.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bandaranayake, R.M. et al., The Effect of Clade-Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways. J.Virol. (2010)

Release Date

2010-08-11

Peptides

HIV-1 Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 Protease