SMTL ID : 3tkw.1

Crystal structure of HIV protease model precursor/Darunavir complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: G.77, T.78, N.92 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: V.15, T.16, A.71 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: G.77, T.78, N.92 Ligands: GOL.5 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Chain A: D.64 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.64 Water bridges: A:P.43, A:R.45, A:R.45, A:D.64

1 x 017: (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE(Non-covalent)

017.3: 22 residues within 4Å: Chain A: L.27, D.29, G.31, A.32, D.33, D.34, G.52, G.53, I.54 Chain B: L.27, D.29, G.31, A.32, D.34, V.36, I.51, G.52, G.53, I.54, P.85, V.86, I.88 22 PLIP interactions: 13 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.27, B:A.32, B:V.36, B:I.51, B:P.85, B:P.85, B:V.86, B:I.88, A:L.27 Hydrogen bonds: B:D.34, B:D.34, B:D.34, B:I.54, A:D.29, A:G.31, A:D.33, A:D.34, A:D.34 Salt bridges: B:D.29, A:D.29 Water bridges: A:I.54, A:I.54

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain B: T.16, I.17, K.18, E.69, I.70, A.71, G.72 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.69, B:E.69, B:E.69, B:G.72 GOL.5: 5 residues within 4Å: Chain B: Q.65, I.76, G.77, Q.96 Ligands: CL.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.65, B:Q.96 Water bridges: B:Q.65, B:I.76, B:G.77, B:T.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agniswamy, J. et al., Terminal interface conformations modulate dimer stability prior to amino terminal autoprocessing of HIV-1 protease. Biochemistry (2012)

Release Date

2012-04-25

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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