SMTL ID : 7ne7.1

oligopeptidase B from S. proteomaculans with modified hinge region in complex with N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

6 x SPM: SPERMINE(Non-covalent)

SPM.1: 7 residues within 4Å: Chain A: Y.450, Y.452, M.459, G.531, S.532, Q.555, V.556 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.556 Hydrogen bonds: A:Q.555 Water bridges: A:Y.452, A:Q.555 SPM.2: 2 residues within 4Å: Chain A: G.207, D.209 No protein-ligand interaction detected (PLIP) SPM.3: 5 residues within 4Å: Chain A: Y.80, Y.100, L.129, L.132, Y.366 No protein-ligand interaction detected (PLIP) SPM.6: 7 residues within 4Å: Chain A: T.386, L.388, K.402, Q.403, Q.404 Ligands: SPM.7, SPM.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.386 SPM.7: 4 residues within 4Å: Chain A: T.386, D.460, A.462 Ligands: SPM.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.462 Hydrogen bonds: A:T.386, A:T.386, A:D.460 SPM.8: 5 residues within 4Å: Chain A: E.331, L.364, A.365, Y.366 Ligands: SPM.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.331

2 x TCK: N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide(Covalent)

TCK.4: 12 residues within 4Å: Chain A: Y.452, Y.455, S.532, A.533, F.558, T.564, L.572, T.573, E.576, W.580, Q.619, V.620 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.564, A:L.572, A:L.572, A:E.576, A:Q.619, A:V.620 Hydrogen bonds: A:A.533 Water bridges: A:V.620 pi-Stacking: A:F.558 TCK.5: 4 residues within 4Å: Chain A: E.96, D.649, H.652, S.656 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., The Crystal Structure of N alpha-p-tosyl-lysyl Chloromethylketone-Bound Oligopeptidase B from Serratia Proteamaculans Revealed a New Type of Inhibitor Binding. Crystals (2021)

Release Date

2021-02-17

Peptides

Oligopeptidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oligopeptidase B

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