SMTL ID : 6ixd.1

X-ray crystal structure of bPI-11 hiv-1 protease complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: K.45, M.46, F.53 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.48 GOL.4: 6 residues within 4Å: Chain B: K.55, V.56, R.57, V.77, G.78, P.79 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.57, B:R.57 Water bridges: B:V.56, B:V.56 GOL.5: 6 residues within 4Å: Chain B: T.12, I.13, K.14, E.65, A.67, G.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.12, B:E.65, B:G.68

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

SO4.2: 2 residues within 4Å: Chain A: P.1, H.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.1 Salt bridges: A:H.69 SO4.6: 2 residues within 4Å: Chain B: K.14, G.17 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.14, B:K.14, B:K.14, B:G.17 Salt bridges: B:K.14

1 x B0F: (4R)-3-[(2S,3S)-3-[2-[4-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-2,6-dimethyl-phenoxy]ethanoylamino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide(Non-covalent)

B0F.3: 26 residues within 4Å: Chain A: 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 Chain B: D.25, G.27, A.28, D.29, D.30, V.32, K.45, I.47, G.48, G.49, I.50, V.82, I.84 24 PLIP interactions: 12 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:D.29, B:D.30, B:V.32, B:I.47, B:I.47, B:V.82, B:I.84, A:A.28, A:D.30, A:V.32, A:I.47, A:P.81, A:V.82, A:I.84 Hydrogen bonds: B:D.25, B:G.27, B:D.29, A:G.27, A:G.27, A:D.29 Water bridges: B:D.29, B:I.50, A:R.8, A:I.50

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain B: T.4, L.5, W.6, K.7 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hidaka, K. et al., Acquired Removability of Aspartic Protease Inhibitors by Direct Biotinylation. Bioconjug.Chem. (2019)

Release Date

2019-05-22

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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