4GMD

The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with AZT Monophosphate

Structural Biology Knowledgebase: 4GMD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 4GMD

Classification: Transferase / Inhibitor

Total Structure Weight: 95553.11

Macromolecule Entities
Molecule Chains Length Organism Details
Thymidylate kinase A, B, C, D 213 Pseudomonas aeruginosa EC#: 2.7.4.9 IUBMB
Gene Name(s): tmk PA2962
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
OIFWQOKDSPDILA-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.177
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 44.50 α = 90.00
b = 123.40 β = 100.00
c = 73.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-15
  • Released Date: 2012-08-29
  • Deposition author(s): Tan, K., Joachimiak, G., Jedrzejczak, R., Sacchettini, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MT

Revision History

No revisions since initial release