Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 227649.53 
• Atom Count: 16641 
• Residue Count: 2004 
• Unique protein chains: 1

3G25

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

• DOI: 10.2210/pdb3G25/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus (strain COL)
• Expression System: Escherichia coli


• Deposited: 2009-01-30 Released: 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)

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Experimental Data Snapshot

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

Literature

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

Minasov, G., Skarina, T., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glycerol kinase	A, B, C, D	501	Staphylococcus aureus (strain COL)	Mutation(s): 0  Gene Names: glpK EC: 2.7.1.30
Find proteins for Q5HGD2 (Staphylococcus aureus (strain COL)) Go to UniProtKB:  Q5HGD2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A, B, C, D	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	A, B, D	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
GOL	A, B, C, D	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.246 
• R-Value Work: 0.193 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 
  10.18430/M33G25 Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 63.750	α = 90.00
b = 193.742	β = 103.60
c = 91.669	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
HKL-2000	data scaling
HKL-2000	data reduction
REFMAC	refinement
Blu-Ice	data collection

Structure Validation

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 

• Version 1.0: 2009-02-17
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description