1K08

Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b

Structural Biology Knowledgebase: 1K08 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 1K08

Classification: TRANSFERASE

Total Structure Weight: 98191.73

Macromolecule Entities
Molecule Chains Length Organism Details
Glycogen Phosphorylase 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
BZD
Query on BZD

A N-BENZOYL-N'-BETA-D-GLUCOPYRANOSYL UREA
C14 H18 N2 O7
JSBCZGSPFATCOV-BZNQNGANSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BZD Ki: 4600 nM (99) BindingDB

Ki: 4600 nM  BindingMOAD
Ki: 4600 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.180
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.52 α = 90.00
b = 128.52 β = 90.00
c = 116.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-18
  • Released Date: 2001-10-03
  • Deposition author(s): Oikonomakos, N.G., Kosmopoulou, M., Zographos, S.E., Leonidas, D.D., Chrysina, E.D., Somsak, L., Nagy, V., Praly, J.P., Docsa, T., Toth, B., Gergely, 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