2VSN

Structure and topological arrangement of an O-GlcNAc transferase homolog: insight into molecular control of intracellular glycosylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of an O-Glcnac Transferase Homolog Provides Insight Into Intracellular Glycosylation.

Martinez-Fleites, C.Macauley, M.S.He, Y.Shen, D.L.Vocadlo, D.J.Davies, G.J.

(2008) Nat Struct Mol Biol 15: 764

  • DOI: 10.1038/nsmb.1443
  • Primary Citation of Related Structures:  
    2VSN

  • PubMed Abstract: 
  • N-Acetylglucosamine (O-GlcNAc) modification of proteins provides a mechanism for the control of diverse cellular processes through a dynamic interplay with phosphorylation. UDP-GlcNAc:polypeptidyl transferase (OGT) catalyzes O-GlcNAc addition. The structure of an intact OGT homolog and kinetic analysis of human OGT variants reveal a contiguous superhelical groove that directs substrates to the active site ...

    N-Acetylglucosamine (O-GlcNAc) modification of proteins provides a mechanism for the control of diverse cellular processes through a dynamic interplay with phosphorylation. UDP-GlcNAc:polypeptidyl transferase (OGT) catalyzes O-GlcNAc addition. The structure of an intact OGT homolog and kinetic analysis of human OGT variants reveal a contiguous superhelical groove that directs substrates to the active site.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XCOGTA, B568Xanthomonas campestris pv. campestris str. 8004Mutation(s): 1 
Gene Names: XC_3364
EC: 2.4
UniProt
Find proteins for A0A0H2XAK3 (Xanthomonas campestris pv. campestris (strain 8004))
Explore A0A0H2XAK3 
Go to UniProtKB:  A0A0H2XAK3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.691α = 90
b = 105.692β = 90
c = 151.036γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance