1EM6

HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP-526,423

Structural Biology Knowledgebase: 1EM6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.233

Literature

Macromolecules
Sequence Display for 1EM6

Classification: TRANSFERASE

Total Structure Weight: 196112.73

Macromolecule Entities
Molecule Chains Length Organism Details
LIVER GLYCOGEN PHOSPHORYLASE A, B 847 Homo sapiens EC#: 2.4.1.1 IUBMB
Mutation: S569R
Gene Name(s): PYGL Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CP4
Query on CP4

A BIS[5-CHLORO-1H-INDOL-2-YL-CARBONYL-AMINOETHYL]- ETHYLENE GLYCOL
CP-526423; 1,2-BIS(2-(5-CHLOROINDOLE-2-CARBONYLAMINO)ETHOXY)ETHANE (Synonym)
C24 H24 Cl2 N4 O4
MWWXABBBAPKJDX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

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

A, B 1-N-ACETYL-BETA-D-GLUCOSAMINE
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

B (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CP4 IC50: 6 nM (94 - 100) BindingDB

IC50: 6 nM  BindingMOAD
IC50: 6 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.233
  • Space Group: P 31

Unit Cell:

Length (Å) Angle (°)
a = 123.31 α = 90.00
b = 123.31 β = 90.00
c = 122.32 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-03-16
  • Released Date: 2000-11-01
  • Deposition author(s): Rath, V.L., Ammirati, M., Danley, D.E., Ekstrom, J.L., Hynes, T.R., Olson, T.V., Hoover, D.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update