3W7W

Crystal structure of E. coli YgjK E727A complexed with 2-O-alpha-D-glucopyranosyl-alpha-D-galactopyranose

Structural Biology Knowledgebase: 3W7W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3W7W

Classification: HYDROLASE

Total Structure Weight: 172829.89

Macromolecule Entities
Molecule Chains Length Organism Details
Uncharacterized protein YgjK A, B 760 Escherichia coli EC#: 3.2.1 IUBMB
Mutation: E727A
Gene Name(s): ygjK b3080 JW3051
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLC
Query on GLC

A, B ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.174
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.88 α = 90.00
b = 138.14 β = 99.03
c = 82.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-08
  • Released Date: 2013-07-17
  • Deposition author(s): Miyazaki, T., Ichikawa, M., Yokoi, G., Kitaoka, M., Mori, H., Kitano, Y., Nishikawa, A., Tonozuka, T.

Revision History

  • 2014-03-12
    Type: Citation | Details: Citation update