SMTL ID : 5cb5.14 (17 other biounits)

Structural Insights into the Mechanism of Escherichia coli Ymdb

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x ZOD: [(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanoate(Non-covalent)

ZOD.1: 21 residues within 4Å: Chain A: G.16, D.17, I.18, A.29, A.31, G.36, G.37, G.38, G.39, V.40, A.41, A.43, A.126, I.127, S.128, T.129, G.130, V.131, Y.132, V.163, Y.165 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.31 Hydrogen bonds: A:D.17, A:I.18, A:G.38, A:G.39, A:V.40, A:S.128, A:T.129, A:G.130, A:V.131, A:Y.132, A:Y.132 Water bridges: A:Y.132 pi-Stacking: A:Y.165, A:Y.165

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.112, F.150, R.153, H.154 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.112, A:R.153, A:H.154

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
M

O-acetyl-ADP-ribose deacetylase

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