4GMD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

Tan, K.Joachimiak, G.Jedrzejczak, R.Sacchettini, J.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate kinase
A, B, C, D
213Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA2962tmk
EC: 2.7.4.9
UniProt
Find proteins for Q9HZN8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HZN8 
Go to UniProtKB:  Q9HZN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HZN8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATM
Query on ATM

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
O [auth D]
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
OIFWQOKDSPDILA-XLPZGREQSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
P [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]
I [auth B]
M [auth C]
N [auth C]
Q [auth D]
F [auth A],
I [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.5α = 90
b = 123.404β = 100
c = 73.92γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description