SMTL ID : 3nwx.1

X-ray structure of ester chemical analogue [O-Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: P.1 Chain B: F.99 No protein-ligand interaction detected (PLIP) SO4.2: 4 residues within 4Å: Chain A: G.73, T.74, N.88, Q.92 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.74, A:T.74, A:T.74, A:N.88, A:N.88, A:Q.92 SO4.4: 3 residues within 4Å: Chain A: R.87 Chain B: K.7, R.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.87 Hydrogen bonds: B:R.8 SO4.5: 8 residues within 4Å: Chain B: T.12, I.13, R.14, L.19, E.65, I.66, A.67, G.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.65, B:G.68 SO4.6: 5 residues within 4Å: Chain A: L.5, W.6 Chain B: R.87, N.88, T.91 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.87

1 x KVS: N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide(Non-covalent)

KVS.3: 23 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, K.45, I.47, G.48, G.49, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, T.80, I.84 28 PLIP interactions: 13 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:I.84, A:I.47, A:V.82, A:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.30, B:D.30, B:D.30, B:D.30, B:G.48, B:G.48, A:R.8, A:D.25, A:G.27, A:D.29, A:D.29, A:D.29, A:D.29, A:G.48, A:G.48 Water bridges: B:D.29, A:R.8, A:R.8, A:K.45 Salt bridges: B:D.29

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

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