7E9J

Crystal Structure of POMGNT2 in complex with UDP

  • Classification: TRANSFERASE
  • Organism(s): Bos taurus
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-03-04 Released: 2021-05-05 
  • Deposition Author(s): Kuwabara, N.
  • Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
A, B
539Bos taurusMutation(s): 0 
Gene Names: POMGNT2, AGO61, GTDC2
EC: 2.4.1.312
UniProt
Find proteins for Q5NDF2 (Bos taurus)
Explore Q5NDF2 
Go to UniProtKB:  Q5NDF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5NDF2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]		URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS (Subject of Investigation/LOI)
Query on TRS
Download Ideal Coordinates CCD File 
F [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.129α = 90
b = 106.233β = 90
c = 132.359γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

  • Released Date: 2021-05-05 
    • Deposition Author(s): Kuwabara, N.
Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP16K07284
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101083
Japan Society for the Promotion of Science (JSPS)JapanJP19H05648
Japan Society for the Promotion of Science (JSPS)JapanJP17H03987

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references