SMTL ID : 7yws.1

Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 3 spermine molecules at 1.7 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

3 x SPM: SPERMINE(Non-covalent)

SPM.1: 7 residues within 4Å: Chain A: E.417, Y.435, F.440, R.442, A.517, Q.518, Y.520 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.520 Hydrogen bonds: A:Y.435, A:R.442, A:R.442, A:Q.518 Water bridges: A:Q.518 SPM.2: 6 residues within 4Å: Chain A: Y.80, Y.100, L.129, G.130, L.132, Y.366 No protein-ligand interaction detected (PLIP) SPM.3: 6 residues within 4Å: Chain A: Y.450, Y.452, M.459, G.531, Q.555, V.556 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.452, A:V.556 Water bridges: A:Y.450, A:Y.450, A:S.457

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Britikov, V.V. et al., Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation. Crystals (2022)

Release Date

2023-01-18

Peptides

Oligopeptidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oligopeptidase B

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