SMTL ID : 4dqb.1

Crystal Structure of wild-type HIV-1 Protease in Complex with DRV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: K.7, R.8, L.10 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.8 Water bridges: A:R.8, A:R.8 EDO.4: 4 residues within 4Å: Chain A: W.6, K.7 Chain B: R.87 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.87, B:R.87

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)

017.2: 25 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.30, V.32, I.47, 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 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:L.23, B:V.82, A:L.23, A:A.28, A:V.32, A:P.81, A:V.82, A:I.84 Hydrogen bonds: B:D.25, B:G.27, B:G.27, B:D.29, B:D.30, A:D.30, A:D.30 Water bridges: B:I.50, B:I.50, A:D.29 Salt bridges: B:D.25, A:D.25

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

PO4.3: 3 residues within 4Å: Chain B: P.1, A.67, H.69 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.1, B:A.67 Salt bridges: B:H.69

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 3 residues within 4Å: Chain B: E.21, V.82, N.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.83 Water bridges: B:E.21 Salt bridges: B:E.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mittal, S. et al., Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease. J.Am.Chem.Soc. (2012)

Release Date

2012-03-07

Peptides

Aspartyl protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartyl protease