SMTL ID : 2oyk.1 (1 other biounit)

Endo-glycoceramidase II from Rhodococcus sp.: cellobiose-like isofagomine complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: N.213, V.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.213, A:V.216 NA.2: 2 residues within 4Å: Chain A: A.153, T.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.156, A:T.156

1 x 9MR: (3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside(Non-covalent)

9MR.3: 11 residues within 4Å: Chain A: S.54, K.57, H.126, D.128, N.149, W.169, E.224, Y.297, E.342, W.373 Ligands: GOL.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.54, A:K.57, A:K.57, A:N.149, A:E.342 Water bridges: A:S.54, A:W.169, A:N.270 Salt bridges: A:K.57

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: W.373, W.380 Ligands: 9MR.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caines, M.E. et al., The structural basis of glycosidase inhibition by five-membered iminocyclitols: the clan a glycoside hydrolase endoglycoceramidase as a model system. Angew.Chem.Int.Ed.Engl. (2007)

Release Date

2007-03-06

Peptides

Endoglycoceramidase II: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoglycoceramidase II

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