2OSX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.139
  • R-Value Work: 0.121

Literature

Macromolecules
Sequence Display for 2OSX

Classification: HYDROLASE

Total Structure Weight: 53472.04

Macromolecule Entities
Molecule Chains Length Organism Details
Endoglycoceramidase II A 481 Rhodococcus sp. EC#: 3.2.1.123 IUBMB
Mutation: E351S
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
16C
Query on 16C

A N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2- YL)PALMITAMIDE
3R,, (2S (Synonym)
C34 H67 N O3
YDNKGFDKKRUKPY-TURZORIXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SIA
Query on SIA

A O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

A BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.139
  • R-Value Work: 0.121
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 77.80 α = 90.00
b = 61.98 β = 112.25
c = 102.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-06
  • Released Date: 2007-02-27
  • Deposition author(s): Caines, M.E.C., Strynadka, N.C.J.

Revision History

  • Version 1_0: 2007-02-27

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance