SMTL ID : 5j14.2 (1 other biounit)

Crystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x BGC- GAL: beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GAL.1: 11 residues within 4Å: Chain A: K.69, H.139, D.141, F.170, N.221, E.222, Y.301, Q.306, D.350, W.373 Ligands: 18C.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.69, A:H.139, A:H.139, A:N.221, A:E.222, A:Q.306, A:Q.306, A:W.373 Water bridges: A:D.141, A:S.347, A:G.148, A:N.150, A:Y.173

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

NA.2: 3 residues within 4Å: Chain A: D.68, D.70, P.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.68

1 x 18C: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE(Non-covalent)

18C.3: 15 residues within 4Å: Chain A: P.171, L.172, Y.174, L.175, E.222, W.224, F.233, V.270, N.273, Q.274, M.275, Y.301, I.303, Q.306 Ligands: BGC-GAL.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.171, A:P.171, A:L.172, A:Y.174, A:Y.174, A:L.175, A:W.224, A:F.233, A:F.233, A:V.270, A:V.270, A:Y.301, A:I.303, A:Q.306 Hydrogen bonds: A:E.222, A:N.273, A:Q.274, A:Q.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, Y.B. et al., Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases. J. Biol. Chem. (2017)

Release Date

2016-04-27

Peptides

Putative secreted endoglycosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Putative secreted endoglycosylceramidase

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