3BD7

Glycogen Phosphorylase complex with 1(-D-glucopyranosyl) thymine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • 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 2.1 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
Find similar proteins by:  (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
Binding Affinity Annotations 
IDSourceBinding Affinity
CKB BindingDB:  3BD7 IC50: 6600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.963α = 90
b = 127.963β = 90
c = 116.23γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary