SMTL ID : 5cb3.1

Structural Insights into the Mechanism of Escherichia coli Ymdb

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.1: 21 residues within 4Å: Chain A: G.16, D.17, I.18, A.29, A.30, N.31, G.36, G.37, G.38, G.39, V.40, D.41, A.43, A.126, I.127, S.128, T.129, G.130, V.131, Y.132, Y.165 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:D.17, A:D.17, A:I.18, A:N.31, A:G.38, A:G.39, A:V.40, A:D.41, A:D.41, A:S.128, A:S.128, A:G.130, A:V.131, A:Y.132, A:N.169 Water bridges: A:D.41, A:D.41, A:A.126, A:R.136, A:R.136, A:Y.165, A:Y.165, A:Y.165 pi-Stacking: A:Y.165, A:Y.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, W. et al., Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase. J.Struct.Biol. (2015)

Release Date

2015-11-04

Peptides

O-acetyl-ADP-ribose deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O-acetyl-ADP-ribose deacetylase