SMTL ID : 4dqg.1

Crystal Structure of apo(G16C/L38C) HIV-1 Protease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-dimer

Ligands

1 x HGU: N-HYDROXYGUANIDINE(Non-covalent)

HGU.1: 5 residues within 4Å: Chain A: R.14, I.15, C.16, G.17, I.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.14, A:C.16, A:G.17, A:I.63

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: D.25, G.27, G.49 Chain B: D.25 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.25 GOL.3: 5 residues within 4Å: Chain A: A.28, D.29, D.30, G.48 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.29, A:D.30 GOL.5: 5 residues within 4Å: Chain B: A.28, D.29, D.30, G.48, G.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.29, B:D.30, B:D.30, B:D.30

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 3 residues within 4Å: Chain A: I.15, C.38, I.62 No protein-ligand interaction detected (PLIP)

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

ACT.6: 2 residues within 4Å: Chain B: P.1, H.69 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.69

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 2 residues within 4Å: Chain B: K.7, R.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.8, B:R.8 Water bridges: A:R.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mittal, S. et al., Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease. J.Am.Chem.Soc. (2012)

Release Date

2012-03-07

Peptides

Aspartyl protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aspartyl protease

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