1P4H

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

Structural Biology Knowledgebase: 1P4H SBKB.org


Experimental Data Snapshot

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

Literature

Macromolecules
Sequence Display for 1P4H

Classification: TRANSFERASE

Total Structure Weight: 97898.33

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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CR6
Query on CR6

A 1-DEOXY-1-ACETYLAMINO-BETA-D-GLUCO-2-HEPTULOPYRANOSONAMIDE
C9 H16 N2 O7
BUPVODXECQDZQR-YCOWOFQRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CR6 Ki: 310000 nM (99) BindingDB

Ki: 310000 nM  BindingMOAD
N/A in PDBbind

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 = 127.98 α = 90.00
b = 127.98 β = 90.00
c = 115.53 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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values