SMTL ID : 4epj.1

Crystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate p2-NC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

1 x ALA- THR- ILE- MET- MET- GLN- ARG- GLY: substrate p2-NC(Non-covalent)

ALA-THR-ILE-MET-MET-GLN-ARG-GLY.1: 25 residues within 4Å: Chain A: N.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, T.80, P.81, I.84, L.127, N.129, G.131, A.132, D.133, D.134, K.149, I.151, G.152, G.153, I.154, P.185, I.188 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:A.28, A:I.47, A:I.50, A:D.134, A:I.151, A:I.154 Hydrogen bonds: A:N.25, A:G.27, A:D.29, A:D.29, A:D.30, A:D.30, A:G.48, A:G.48, A:I.50, A:N.129, A:G.131, A:D.133, A:D.133, A:D.133, A:G.152, A:G.152 Water bridges: A:I.154

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: W.6, D.133, D.134, R.191, N.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.133, A:D.134, A:R.191, A:R.191 GOL.5: 6 residues within 4Å: Chain A: D.29, R.87, N.88, T.91, L.109, W.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.87, A:R.87, A:W.110 Water bridges: A:N.88

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: G.73, T.74, N.88 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.74, A:T.74, A:N.88 Water bridges: A:N.88, A:Q.92

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

DMS.4: 2 residues within 4Å: Chain A: K.7, R.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.8

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

ACT.6: 2 residues within 4Å: Chain A: K.124, E.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.125, A:N.187

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.7: 3 residues within 4Å: Chain A: R.87, K.111, R.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alvizo, O. et al., Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease. Protein Sci. (2012)

Release Date

2012-06-06

Peptides

protease, tethered dimer: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

protease, tethered dimer

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