2OYK

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

• PDB DOI: https://doi.org/10.2210/pdb2OYK/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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.198 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

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

---

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: 105.05 kDa 
• Atom Count: 7,936 
• Modelled Residue Count: 879 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9MR	E [auth A], I [auth B]	(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside C12 H23 N O8 LEOSSOWHBSKZSO-WUYFHPBOSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A], D [auth A], G [auth B], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9MR	PDBBind:  2OYK	Ki: 5000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.198 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.545	α = 90
b = 92.919	β = 98.32
c = 94.489	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary