1P4H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.Biotransfor. 21: 233-242


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, muscle form
A
842Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Go to Gene View: PYGM
Go to UniProtKB:  P00489
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CR6
Query on CR6

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Download CCD File 
A
1-DEOXY-1-ACETYLAMINO-BETA-D-GLUCO-2-HEPTULOPYRANOSONAMIDE
C9 H16 N2 O7
BUPVODXECQDZQR-YCOWOFQRSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CR6Ki: 310000 nM (99) BINDINGDB
CR6Ki: 310000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 127.980α = 90.00
b = 127.980β = 90.00
c = 115.529γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description