2H39

Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.176 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADQClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose

McCoy, J.G.Wesenberg, G.E.Phillips Jr., G.N.Bitto, E.Bingman, C.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable galactose-1-phosphate uridyl transferase
A, B
351Arabidopsis thalianaMutation(s): 1 
Gene Names: At5g18200
EC: 2.7.7.12 (PDB Primary Data), 2.7.7 (UniProt)
UniProt
Find proteins for Q9FK51 (Arabidopsis thaliana)
Explore Q9FK51 
Go to UniProtKB:  Q9FK51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FK51
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADQ
Query on ADQ

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
ADENOSINE-5'-DIPHOSPHATE-GLUCOSE
C16 H25 N5 O15 P2
WFPZSXYXPSUOPY-ROYWQJLOSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.318α = 90
b = 95.454β = 90
c = 110.504γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADQClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-25
    Changes: Data collection
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description