SMTL ID : 1yoe.2 (3 other biounits)

Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x RIB: alpha-D-ribofuranose(Non-covalent)

RIB.1: 13 residues within 4Å: Chain A: D.25, D.26, N.50, T.135, M.161, N.169, E.175, F.176, N.177, L.200, H.251, D.252 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.25, A:N.50, A:N.169, A:N.169, A:N.177 RIB.3: 13 residues within 4Å: Chain B: D.25, D.26, N.50, T.135, M.161, N.169, E.175, F.176, N.177, L.200, H.251, D.252 Ligands: CA.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.25, B:N.50, B:N.169, B:N.169, B:E.175, B:N.177

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.21, D.26, N.50, T.135, D.252 Ligands: RIB.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.21, A:D.26, A:T.135, A:D.252, H2O.1 CA.4: 6 residues within 4Å: Chain B: D.21, D.26, N.50, T.135, D.252 Ligands: RIB.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.21, B:D.26, B:T.135, B:D.252, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muzzolini, L. et al., Crystal structure of the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose. To be Published

Release Date

2006-01-17

Peptides

Hypothetical protein ybeK: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypothetical protein ybeK

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