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 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UDPClick on this verticalbar to view details

This is version 1.3 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: https://doi.org/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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
XCOGT
A, B
568Xanthomonas campestris pv. campestris str. 8004Mutation(s): 1 
EC: 2.4 (PDB Primary Data), 2.4.1.255 (UniProt)
UniProt
Find proteins for A0A0H2XAK3 (Xanthomonas campestris pv. campestris (strain 8004))
Explore A0A0H2XAK3 
Go to UniProtKB:  A0A0H2XAK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2XAK3
Sequence Annotations
Expand
  • Reference Sequence
2VSN_1
050100150200250300350400450500550
2VSN_1
UNIPROT A0A0H2XAK3
UNMODELED
MUTATION
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.265 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UDPClick on this verticalbar to view details

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
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other