Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 330.88 kDa 
• Atom Count: 22,524 
• Modelled Residue Count: 2,836 
• Deposited Residue Count: 2,936 
• Unique protein chains: 2

 4AY5

Human O-GlcNAc transferase (OGT) in complex with UDP and glycopeptide

• PDB DOI:  https://doi.org/10.2210/pdb4AY5/pdb

• Classification: TRANSFERASE/PEPTIDE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-06-18 Released: 2012-10-24 
• Deposition Author(s): Schimpl, M., Zheng, X., Blair, D.E., Schuettelkopf, A.W., Navratilova, I., Aristotelous, T., Ferenbach, A.T., Macnaughtan, M.A., Borodkin, V.S., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.204 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

O-Glcnac Transferase Invokes Nucleotide Sugar Pyrophosphate Participation in Catalysis

Schimpl, M., Zheng, X., Borodkin, V.S., Blair, D.E., Ferenbach, A.T., Schuettelkopf, A.W., Navratilova, I., Aristotelous, T., Albarbarawi, O., Robinson, D.A., Macnaughtan, M.A., Van Aalten, D.M.F.

(2012) Nat Chem Biol 8: 969

• PubMed: 23103942 
• DOI: https://doi.org/10.1038/nchembio.1108
• Primary Citation of Related Structures:  
  4AY5, 4AY6


• PubMed Abstract: 
  

Protein O-GlcNAcylation is an essential post-translational modification on hundreds of intracellular proteins in metazoa, catalyzed by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) using unknown mechanisms of transfer and substrate recognition. Through crystallographic snapshots and mechanism-inspired chemical probes, we define how human OGT recognizes the sugar donor and acceptor peptide and uses a new catalytic mechanism of glycosyl transfer, involving the sugar donor α-phosphate as the catalytic base as well as an essential lysine. This mechanism seems to be a unique evolutionary solution to the spatial constraints imposed by a bulky protein acceptor substrate and explains the unexpected specificity of a recently reported metabolic OGT inhibitor.

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Organizational Affiliation: 

College of Life Sciences, University of Dundee, Dundee, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT	A, B, C, D	723	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTAB1TIDE	E [auth I], F [auth J], G [auth K], H [auth L]	11	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15750 (Homo sapiens) Explore Q15750  Go to UniProtKB:  Q15750
PHAROS:  Q15750

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	I [auth A], J [auth B], K [auth C], L [auth D]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NAG	M [auth I], N [auth J], O [auth K], P [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UDP	PDBBind:  4AY5	Kd: 540 (nM) from 1 assay(s)
	BindingDB:  4AY5	IC50: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.204 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 274.17	α = 90
b = 274.17	β = 90
c = 142.15	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Schimpl, M., Zheng, X., Blair, D.E., Schuettelkopf, A.W., Navratilova, I., Aristotelous, T., Ferenbach, A.T., Macnaughtan, M.A., Borodkin, V.S., van Aalten, D.M.F.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references
• Version 1.2: 2012-12-12
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary