SMTL ID : 3tof.1

HIV-1 Protease - Epoxydic Inhibitor Complex (pH 6 - Orthorombic Crystal form P212121)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

1 x 076: (S)-N-((1R,2S)-1-((2R,3R)-3-benzyloxiran-2-yl)-1-hydroxy-3-phenylpropan-2-yl)-3-methyl-2-(2-phenoxyacetamido)butanamide(Non-covalent)

076.1: 20 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, G.49, I.50, P.81, V.82, I.84 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.23, A:P.81, A:V.82, B:L.23, B:P.81, B:P.81, B:V.82, B:I.84 Hydrogen bonds: A:D.25, A:G.27, A:D.29, A:G.48 Water bridges: A:G.48, A:I.50, B:I.50

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 2 residues within 4Å: Chain A: K.45, M.46 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.45 Salt bridges: A:K.45 ACT.4: 2 residues within 4Å: Chain B: R.41, W.42 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.42 Hydrogen bonds: B:W.42

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

DMS.3: 6 residues within 4Å: Chain A: K.14, I.15, G.16, G.17, I.63, E.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.14, A:G.17 DMS.5: 7 residues within 4Å: Chain B: K.14, I.15, G.16, G.17, I.63, I.64, E.65 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olajuyigbe, F.M. et al., Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals. Molecules (2016)

Release Date

2012-08-15

Peptides

Gag-Pol polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gag-Pol polyprotein

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