SMTL ID : 6dj5.1

HIV-1 protease with mutation L76V in complex with GRL-0519 (tris-tetrahydrofuran as P2 ligand)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 1 residues within 4Å: Chain A: D.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 NA.6: 2 residues within 4Å: Chain B: D.60 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.60

5 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.7: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: V.11, T.12, A.67 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: K.7, R.8 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: K.45, M.46, F.53 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.45, A:G.48 GOL.4: 8 residues within 4Å: Chain A: K.14, I.15, G.16, G.17, I.63, I.64, E.65, K.70 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.14, A:G.16, A:G.17, A:E.65, A:K.70, A:K.70 Water bridges: A:I.63 GOL.11: 4 residues within 4Å: Chain A: W.6 Chain B: D.29, R.87, N.88 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:W.6, B:D.29, B:R.87, B:R.87 Water bridges: B:T.91 GOL.12: 6 residues within 4Å: Chain B: R.41, K.43, Q.58, Y.59, D.60 Ligands: NA.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.58, B:D.60, B:D.60, B:D.60

1 x G52: (3R,3aS,3bR,6aS,7aS)-octahydrodifuro[2,3-b:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate(Non-covalent)

G52.5: 25 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, P.81, V.82, I.84 Chain B: D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, V.82, I.84 20 PLIP interactions: 11 interactions with chain A, 9 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:V.82, B:I.84 Hydrogen bonds: A:D.29, A:D.30, A:I.50, B:D.25, B:G.27, B:G.27, B:D.29, B:D.30 Salt bridges: A:R.8, A:D.25, B:D.25 Water bridges: B:I.50

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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