SMTL ID : 3w7w.1 (1 other biounit)

Crystal structure of E. coli YgjK E727A complexed with 2-O-alpha-D-glucopyranosyl-alpha-D-galactopyranose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x GLA- GLC: alpha-D-glucopyranose-(1-2)-alpha-D-galactopyranose(Non-covalent)

GLA-GLC.1: 14 residues within 4Å: Chain A: P.308, W.321, W.323, D.324, D.368, L.369, N.386, K.391, W.496, G.499, D.501, W.680, F.742, W.744 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.391, A:K.391, A:D.501, A:W.323, A:G.499 Water bridges: A:D.501, A:W.680

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.431, N.433, N.435, V.437, E.439, E.549 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.431, A:V.437, A:E.439, A:E.549

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: D.501 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.501, H2O.6, H2O.8, H2O.15, H2O.18, H2O.18 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: E.566 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.566, H2O.5, H2O.9, H2O.12, H2O.13, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazaki, T. et al., Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity. Febs J. (2013)

Release Date

2013-07-17

Peptides

Uncharacterized protein YgjK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized protein YgjK

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