6Q4M

Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.176 (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 PO4Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation

Gundogdu, M.van Aalten, D.M.F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit723Homo sapiensMutation(s): 1 
Gene Names: OGT
EC: 2.4.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for O15294 (Homo sapiens)
Explore O15294 
Go to UniProtKB:  O15294
PHAROS:  O15294
GTEx:  ENSG00000147162 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15294
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
12V
Query on 12V

Download Ideal Coordinates CCD File 
B [auth A](2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
C17 H27 N3 O16 P2 S
JPRVHSQHWXZSNC-UBDZBXRQSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.316α = 90
b = 150.736β = 90
c = 199.492γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

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 PO4Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom110061

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references