4GYW

Crystal structure of human O-GlcNAc Transferase in complex with UDP and a glycopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 4GYW

Classification: transferase / peptide

Total Structure Weight: 166285.06

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit A, C 723 Homo sapiens EC#: 2.4.1.255 IUBMB
Gene Name(s): OGT Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Casein kinase II subunit alpha B, D 14 Homo sapiens EC#: 2.7.11.1 IUBMB
Gene Name(s): CSNK2A1 Gene View CK2A1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UDP
Query on UDP

A, C URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

B, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.187
  • Space Group: I 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 99.00 α = 90.00
b = 137.77 β = 102.90
c = 153.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-05
  • Released Date: 2012-10-31
  • Deposition author(s): Lazarus, M.B., Jiang, J., Gloster, T.M., Zandberg, W.F., Vocadlo, D.J., Walker, S.

Revision History

  • Version 1_0: 2012-10-31

    Type: Initial release

  • Version 1_1: 2012-12-12

    Type: Database references