3G25

1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 3G25

Classification: TRANSFERASE

Total Structure Weight: 227652.16

Macromolecule Entities
Molecule Chains Length Organism Details
Glycerol kinase A, B, C, D 501 Staphylococcus aureus EC#: 2.7.1.30 IUBMB
Gene Name(s): glpK SACOL1320
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A, B, C, D PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 63.75 α = 90.00
b = 193.74 β = 103.60
c = 91.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-01-30
  • Released Date: 2009-02-17
  • Deposition author(s): Minasov, G., Skarina, T., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4