6E4Q

Crystal Structure of the Drosophila Melanogaster Polypeptide N-Acetylgalactosaminyl Transferase PGANT9A in Complex with UDP and Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.799 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A molecular switch orchestrates enzyme specificity and secretory granule morphology.

Ji, S.Samara, N.L.Revoredo, L.Zhang, L.Tran, D.T.Muirhead, K.Tabak, L.A.Ten Hagen, K.G.

(2018) Nat Commun 9: 3508-3508


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
polypeptide N-acetylgalactosaminyltransferase 9
A, B, C, D
510Drosophila melanogasterMutation(s): 0 
Gene Names: pgant9
EC: 2.4.1.41
Find proteins for Q8MRC9 (Drosophila melanogaster)
Go to UniProtKB:  Q8MRC9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, B, C, D
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.799 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.190 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 126.286α = 90.00
b = 168.756β = 106.28
c = 153.099γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHENIXphasing
Aimlessdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release