SMTL ID : 3nyg.1

X-ray structure of ester chemical analogue [O-Gly51,O-Gly51']HIV-1 protease complexed with MVT-101 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

1 x 2NC: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide(Non-covalent)

2NC.1: 27 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: R.8, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, P.81, V.82, I.84 27 PLIP interactions: 14 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:L.23, A:D.30, A:I.47, A:I.50, A:I.50, A:P.81, B:A.28, B:I.50, B:P.81, B:I.84 Hydrogen bonds: A:R.8, A:G.27, A:D.29, A:G.48, A:G.48, B:G.27, B:D.29, B:D.29, B:D.30, B:D.30, B:G.48, B:G.48 Water bridges: A:R.8, A:G.48, A:G.48, B:I.50, B:I.50

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: K.45, L.46 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.45 SO4.3: 1 residues within 4Å: Chain B: R.14 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.14 SO4.4: 1 residues within 4Å: Chain B: Q.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.92 Water bridges: B:G.94, B:G.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torbeev, V.Y. et al., Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-11-02

Peptides

protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

protease