SMTL ID : 7ywz.1

Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 4 spermine molecules at 1.75 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

4 x SPM: SPERMINE(Non-covalent)

SPM.1: 7 residues within 4Å: Chain A: Y.450, Y.452, S.457, M.459, G.531, Q.555, V.556 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.452 SPM.2: 7 residues within 4Å: Chain A: Y.80, Y.100, L.129, G.130, G.131, L.132, Y.366 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.129 Water bridges: A:Y.80, A:L.132, A:L.132, A:Y.366 SPM.3: 4 residues within 4Å: Chain A: E.168, G.207, D.209, P.210 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.209, A:D.209 SPM.4: 6 residues within 4Å: Chain A: S.458, M.459, D.460, A.462, R.467, F.477 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.467

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Y.455, L.572, Q.619 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.619

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrenko, D.E. et al., Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 4 spermine molecules at 1.75 A resolution. To Be Published

Release Date

2023-02-22

Peptides

Oligopeptidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oligopeptidase B

Related Entries With Identical Sequence