SMTL ID : 7vgb.2 (1 other biounit)

Crystal structure of apo prolyl oligopeptidase from Microbulbifer arenaceous

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: K.370, M.391, G.392, N.412, V.446, F.462 No protein-ligand interaction detected (PLIP) GOL.2: 5 residues within 4Å: Chain A: R.492, F.493, Y.494, T.495, R.496 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.492, A:R.492, A:T.495, A:R.496, A:R.496

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 3 residues within 4Å: Chain A: D.34, D.66, W.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.34 Water bridges: A:D.34, A:D.66 TRS.4: 4 residues within 4Å: Chain A: F.198, F.273, Y.276, N.600 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.600 Water bridges: A:F.198, A:Y.276, A:Y.276, A:N.600

1 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 1 residues within 4Å: Chain A: Y.113 No protein-ligand interaction detected (PLIP)

1 x TMO: trimethylamine oxide(Non-covalent)

TMO.6: 6 residues within 4Å: Chain A: Y.482, F.485, S.562, N.563, W.604, Y.608 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.482, A:Y.482, A:N.563 pi-Cation interactions: A:F.485, A:W.604

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, P. et al., The structure and molecular dynamics of prolyl oligopeptidase from Microbulbifer arenaceous provide insights into catalytic and regulatory mechanisms. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-05-25

Peptides

prolyl oligopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

prolyl oligopeptidase

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