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: 2.0 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 1P4J

Classification: TRANSFERASE

Total Structure Weight: 97761.52

Macromolecule Entities
Molecule Chains Length Organism Details
Glycogen phosphorylase, muscle form A 842 Oryctolagus cuniculus EC#: 2.4.1.1 IUBMB
Mutation: L380I
Gene Name(s): PYGM Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PLP
Query on PLP

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CBF
Query on CBF

A C-(1-HYDROGYL-BETA-D-GLUCOPYRANOSYL) FORMAMIDE
C7 H13 N O7
DTZYCNDAJQDPQC-UHKLXPPTSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CBF N/A in BindingDB
Ki: 880000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.181
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.16 α = 90.00
b = 128.16 β = 90.00
c = 116.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-23
  • Released Date: 2004-05-18
  • Deposition author(s): Chrysina, E.D., Oikonomakos, N.G., Zographos, S.E., Kosmopoulou, M.N., Bischler, N., Leonidas, D.D., Nagy, V., Somsak, L., Gergely, P., Praly, J.-P.

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