SMTL ID : 4eq0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

ALA-THR-ILE-MET-MET-GLN-ARG.1: 25 residues within 4Å: Chain A: R.8, L.23, N.25, G.27, S.28, D.29, F.30, V.32, K.45, I.47, R.48, G.49, I.50, V.82, I.84, R.112, N.129, G.131, S.132, D.133, D.134, I.151, T.184, P.185, I.188 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.30, A:I.47, A:I.47 Hydrogen bonds: A:R.8, A:N.25, A:G.27, A:D.29, A:D.29, A:K.45, A:K.45, A:R.48, A:R.48, A:N.129, A:G.131, A:D.133, A:D.134, A:D.134

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

BME.2: 3 residues within 4Å: Chain A: K.111, R.112, L.114 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain A: G.172, H.173, K.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174 EDO.5: 4 residues within 4Å: Chain A: W.6, K.7, R.8, R.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.8, A:R.191, A:R.191 EDO.7: 3 residues within 4Å: Chain A: L.114, V.115, T.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.116, A:T.116

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.6, D.133, R.191, N.192 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.195, A:T.195 GOL.8: 5 residues within 4Å: Chain A: W.146, P.148, K.149, K.159, V.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.149, A:K.149, A:V.160 Water bridges: A:R.161 GOL.9: 6 residues within 4Å: Chain A: T.4, L.5, W.6, T.195, M.199, T.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.5, A:M.199

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

ACT.6: 3 residues within 4Å: Chain A: T.91, Q.92, W.110 No protein-ligand interaction detected (PLIP)

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

PO4.10: 4 residues within 4Å: Chain A: R.118, G.120, G.121, P.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.120, A:G.121 Water bridges: A:P.167

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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