SMTL ID : 6kmp.1

100K X-ray structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with tetrahedral intermediate mimic KVS-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

homo-dimer

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: 30 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, I.32, V.47, G.48, G.49, I.50, P.81, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, I.32, V.47, G.48, G.49, I.50, G.52, F.53, P.81, I.82, I.84 34 PLIP interactions: 17 interactions with chain B, 17 interactions with chain A Hydrophobic interactions: B:A.28, B:I.32, B:P.81, B:I.82, B:I.84, B:I.84, A:L.23, A:D.30, A:I.32, A:V.47, A:I.50, A:P.81, A:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.29, B:D.30, B:D.30, B:D.30, B:G.48, B:G.48, B:G.48, B:G.49, B:I.50, A:G.27, A:G.27, A:D.29, A:G.48, A:G.48 Water bridges: A:D.29, A:G.48, A:G.48, A:I.50, A:P.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, M. et al., Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design. Acs Omega (2020)

Release Date

2020-07-29

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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