2OYK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structural basis of glycosidase inhibition by five-membered iminocyclitols: the clan a glycoside hydrolase endoglycoceramidase as a model system.

Caines, M.E.Hancock, S.M.Tarling, C.A.Wrodnigg, T.M.Stick, R.V.Stutz, A.E.Vasella, A.Withers, S.G.Strynadka, N.C.

(2007) Angew.Chem.Int.Ed.Engl. 46: 4474-4476


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoglycoceramidase II
A, B
481Rhodococcus spMutation(s): 0 
EC: 3.2.1.123
Find proteins for O33853 (Rhodococcus sp)
Go to UniProtKB:  O33853
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
9MR
Query on 9MR

Download SDF File 
Download CCD File 
A, B
(3R,4R,5R)-3-HYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-4-YL BETA-D-GLUCOPYRANOSIDE
CELLOBIOSE-LIKE ISOFAGOMINE
C12 H23 N O8
LEOSSOWHBSKZSO-WUYFHPBOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9MRKi: 5000 nM BINDINGMOAD
9MRKi: 5000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.545α = 90.00
b = 92.919β = 98.32
c = 94.489γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4data scaling
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2007-10-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance