3BCR

Glycogen Phosphorylase b in complex with AZT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 


Literature

D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b

Cisma, C., Sovantzis, D.A., Hadjiloi, T., Stathis, D., Gimisis, T., Hayes, J.M., Zographos, S.E., Leonidas, D.D., Chrysina, E.D., Oikonomakos, N.G.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form842Oryctolagus cuniculusMutation(s): 0 
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AZZ
Query on AZZ
Download Ideal Coordinates CCD File 
B [auth A]3'-azido-3'-deoxythymidine
C10 H13 N5 O4
HBOMLICNUCNMMY-XLPZGREQSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.436α = 90
b = 128.436β = 90
c = 116.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-07-18
    Changes: Non-polymer description
  • Version 1.3: 2023-08-02
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2023-08-16
    Changes: Data collection
  • Version 1.5: 2023-11-01
    Changes: Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection