SMTL ID : 3nxn.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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.1: 28 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84, R.112, L.127, D.129, G.131, A.132, D.133, D.134, I.151, G.152, G.153, X.154, T.184, V.186, I.188 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.32, A:I.47, A:I.50, A:I.50, A:P.81, A:L.127, A:A.132, A:I.151, A:I.188 Hydrogen bonds: A:R.8, A:R.8, A:G.27, A:G.27, A:D.29, A:G.48, A:G.48, A:G.48, A:G.48, A:G.131, A:D.133, A:D.134, A:D.134, A:D.134, A:G.152, A:G.152

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

SO4.2: 5 residues within 4Å: Chain A: L.114, E.125, A.126, V.186, N.187 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.125, A:E.125, A:N.187, A:N.187 Water bridges: A:E.125 SO4.3: 5 residues within 4Å: Chain A: R.14, I.15, G.16, G.17, P.63 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.16, A:G.17 Water bridges: A:R.14, A:R.14, A:R.14, A:P.63 Salt bridges: A:R.14 SO4.4: 2 residues within 4Å: Chain A: K.45, L.46 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.45 SO4.5: 8 residues within 4Å: Chain A: T.116, I.117, R.118, L.123, E.169, I.170, A.171, G.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.172

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 covalent dimer: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

protease covalent dimer

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