2OYM

Endo-glycoceramidase II from Rhodococcus sp.: five-membered iminocyclitol complex

• PDB DOI: https://doi.org/10.2210/pdb2OYM/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus sp. (in: high G+C Gram-positive bacteria)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-22 Released: 2007-03-06 
• Deposition Author(s): Caines, M.E.C., Strynadka, N.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Model: experimental

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

• PubMed: 17487923 
• DOI: https://doi.org/10.1002/anie.200700268
• Primary Citation of Related Structures:  
  2OYK, 2OYL, 2OYM

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 104.91 kDa 
• Atom Count: 7,494 
• Modelled Residue Count: 868 
• Deposited Residue Count: 962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglycoceramidase II	A, B	481	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 0  EC: 3.2.1.123
UniProt
Find proteins for O33853 (Rhodococcus sp) Explore O33853  Go to UniProtKB:  O33853

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNI	D [auth A], F [auth B]	N-{[(2R,3R,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PYRROLIDIN-2-YL]METHYL}-4-(DIMETHYLAMINO)BENZAMIDE C15 H23 N3 O4 OULLPOCYJLHTGG-AAVRWANBSA-N
NA	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MNI	PDBBind:  2OYM	Ki: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.786	α = 90
b = 93.282	β = 98.3
c = 94.471	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Caines, M.E.C., Strynadka, N.C.J.

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2007-10-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2023-08-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description