SMTL ID : 7vgb.1 (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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Q.347, K.348, D.349, Y.365, K.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.348, A:D.349, A:D.349 GOL.2: 2 residues within 4Å: Chain A: R.458, W.522 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.518, A:Y.518 GOL.3: 4 residues within 4Å: Chain A: K.205, D.263, D.400, D.402 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.205, A:D.400, A:D.402 Water bridges: A:D.263 GOL.4: 5 residues within 4Å: Chain A: R.492, F.493, Y.494, T.495, R.496 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.492, A:R.492, A:T.495, A:T.495, A:R.496, A:R.496 GOL.5: 4 residues within 4Å: Chain A: F.198, F.273, Y.276, N.600 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.276 Water bridges: A:Y.276, A:R.648

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 3 residues within 4Å: Chain A: L.343, D.379, G.380 No protein-ligand interaction detected (PLIP)

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

TRS.7: 10 residues within 4Å: Chain A: E.317, T.318, N.319, T.323, N.324, G.325, L.351, N.486, S.516, G.520 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.318, A:N.319, A:L.351, A:N.486, A:S.516 TRS.8: 5 residues within 4Å: Chain A: D.34, D.66, W.67, A.70 Ligands: PEG.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.34, A:D.66 Water bridges: A:D.34, A:D.34

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 5 residues within 4Å: Chain A: A.36, V.38, W.55, L.63 Ligands: TRS.8 No protein-ligand interaction detected (PLIP) PEG.10: 6 residues within 4Å: Chain A: D.206, S.208, Y.211, F.233, Q.244, I.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.244 Water bridges: A:S.208

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

NI.11: 1 residues within 4Å: Chain A: Y.113 No protein-ligand interaction detected (PLIP)

1 x TMO: trimethylamine oxide(Non-covalent)

TMO.12: 6 residues within 4Å: Chain A: Y.482, F.485, S.562, N.563, W.604, Y.608 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.482, A:N.563 pi-Cation interactions: A:F.485

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
A

prolyl oligopeptidase

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