SMTL ID : 6dj7.1

HIV-1 protease with mutation L76V in complex with GRL-5010 (gem-difluoro-bis-tetrahydrofuran as P2 ligand)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

homo-dimer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: D.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 Water bridges: A:R.41

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

CL.2: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: W.6 Ligands: ACT.9 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: P.44, K.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55, A:K.55 GOL.7: 5 residues within 4Å: Chain B: T.12, E.65, I.66, A.67, G.68 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.65, B:G.68 Water bridges: B:T.12, B:T.12

1 x G10: (3R,3aS,6aS)-4,4-difluorohexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate(Non-covalent)

G10.4: 25 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.30, V.32, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, V.82, I.84 25 PLIP interactions: 11 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:V.32, A:P.81, A:V.82, A:I.84, B:L.23, B:I.50, B:V.82, B:I.84 Hydrogen bonds: A:D.30, A:D.30, A:I.50, B:D.25, B:G.27, B:G.27, B:D.29, B:D.30 Water bridges: A:D.29, B:I.50, B:I.50, B:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

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

ACT.8: 5 residues within 4Å: Chain B: P.39, G.40, R.41, Y.59, D.60 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.60 Hydrogen bonds: B:D.60 Water bridges: B:R.41 ACT.9: 3 residues within 4Å: Chain B: T.4, W.6 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.4 Hydrogen bonds: B:T.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong-Sam, A. et al., Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease. ACS Omega (2018)

Release Date

2018-10-17

Peptides

HIV-1 protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 protease

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