1P4J

Crystal structure of glycogen phosphorylase b in complex with C-(1-hydroxy-beta-D-glucopyranosyl)formamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crsytallographic Studies on alpha- and beta-D-glucopyranosyl Formamide Analogues, Inhibitors of Glycogen Phosphorylase

Chrysina, E.D.Oikonomakos, N.G.Zographos, S.E.Kosmopoulou, M.N.Bischler, N.Leonidas, D.D.Kovacs, L.Docsa, T.Gergely, P.Somsak, L.

(2003) Biocatal Biotransformation 21: 233-242


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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
CBF
Query on CBF

Download Ideal Coordinates CCD File 
C [auth A](2R,3R,4S,5S,6R)-2,3,4,5-tetrahydroxy-6-(hydroxymethyl)oxane-2-carboxamide
C7 H13 N O7
DTZYCNDAJQDPQC-UHKLXPPTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.16α = 90
b = 128.16β = 90
c = 116.01γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary