SMTL ID : 4eqj.1

Crystal Structure of inactive single chain variant of HIV-1 Protease in Complex with the substrate RT-RH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x GLU- THR- PHE- TYR- VAL- ASP: substrate RT-RH(Non-covalent)

GLU-THR-PHE-TYR-VAL-ASP.1: 25 residues within 4Å: Chain A: R.8, N.25, G.27, S.28, D.29, F.30, V.32, R.48, P.81, V.82, I.84, R.112, L.127, N.129, G.131, S.132, D.133, V.136, I.151, G.152, G.153, I.154, P.185, V.186, I.188 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:V.32, A:P.81, A:V.82, A:I.84, A:L.127, A:V.136, A:I.151, A:I.154, A:P.185, A:V.186, A:I.188 Hydrogen bonds: A:N.25, A:G.27, A:D.29, A:D.29, A:N.129, A:G.131, A:D.133, A:D.134, A:G.152, A:G.152 Water bridges: A:R.48, A:R.48

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

EDO.2: 6 residues within 4Å: Chain A: K.41, W.42, K.43, Q.58, Y.59, D.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.58, A:D.60 EDO.3: 3 residues within 4Å: Chain A: T.91, T.96, W.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.91 EDO.4: 3 residues within 4Å: Chain A: R.87, K.111, R.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.87, A:R.112 EDO.5: 3 residues within 4Å: Chain A: R.118, G.121, E.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.121, A:E.169 EDO.6: 3 residues within 4Å: Chain A: G.155, G.156, F.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.157 EDO.7: 5 residues within 4Å: Chain A: W.6, G.101, T.195, Q.196, G.198 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: R.14, G.16, G.17, P.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.17 Water bridges: A:G.16

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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