6Q4M

Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation

• PDB DOI: https://doi.org/10.2210/pdb6Q4M/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-12-06 Released: 2019-12-25 
• Deposition Author(s): Gundogdu, M., van Aalten, D.M.F.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.199 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation

Gundogdu, M., van Aalten, D.M.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 81.84 kDa 
• Atom Count: 5,948 
• Modelled Residue Count: 698 
• Deposited Residue Count: 723 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A	723	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
12V	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)	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 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.316	α = 90
b = 150.736	β = 90
c = 199.492	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Gundogdu, M., van Aalten, D.M.F.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	110061

Revision History  

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