SMTL ID : 2osx.1

Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

1 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-SIA.1: 13 residues within 4Å: Chain A: S.54, K.57, H.126, D.128, A.146, I.147, N.149, W.169, N.223, E.224, W.373, W.380 Ligands: 16C.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.57, A:H.126, A:D.128, A:N.223, A:S.54, A:K.57, A:D.128, A:I.147, A:N.149, A:W.373 Water bridges: A:S.342, A:S.54, A:S.54, A:A.146, A:S.54, A:R.168, A:W.169, A:E.170, A:E.170

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

NA.2: 2 residues within 4Å: Chain A: N.213, V.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.216, A:V.216 NA.3: 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 NA.4: 2 residues within 4Å: Chain A: D.282, Q.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.282, A:Q.288 NA.5: 1 residues within 4Å: Chain A: P.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.60, A:R.90

1 x 16C: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE(Non-covalent)

16C.6: 12 residues within 4Å: Chain A: R.168, W.169, E.170, Y.173, E.224, A.266, I.267, N.270, Q.271, Y.297, D.302 Ligands: BGC-GAL-SIA.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.170, A:Y.173, A:A.266 Hydrogen bonds: A:E.224, A:N.270, A:Q.271 Water bridges: A:E.170, A:D.302

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: P.96, W.154, Y.157, E.194, L.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.194 Water bridges: A:H.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caines, M.E. et al., Structural and Mechanistic Analyses of endo-Glycoceramidase II, a Membrane-associated Family 5 Glycosidase in the Apo and GM3 Ganglioside-bound Forms. J.Biol.Chem. (2007)

Release Date

2007-02-27

Peptides

Endoglycoceramidase II: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoglycoceramidase II