2PYW

Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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This is version 2.1 of the entry. See complete history. 


Literature

Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR reveals a more occluded active site than its bacterial homolog

Ku, S.Y., Cornell, K.A., Howell, P.L.

(2007) BMC Struct Biol 7: 70-70

  • DOI: https://doi.org/10.1186/1472-6807-7-70
  • Primary Citation of Related Structures:  
    2PYW

  • PubMed Abstract: 

    Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target for the design of specific herbicides or antibiotics.

    • Organizational Affiliation: 

    Program in Molecular Structure and Function, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, M5G 1X8, CANADA. syku@sickkids.ca


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
420Arabidopsis thalianaMutation(s): 0 
Gene Names: F10F5.1
EC: 2.7.1.100
UniProt
Find proteins for Q9C6D2 (Arabidopsis thaliana)
Explore Q9C6D2 
Go to UniProtKB:  Q9C6D2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C6D2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SR1
Query on SR1
Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]		5-S-methyl-5-thio-alpha-D-ribofuranose
C6 H12 O4 S
OLVVOVIFTBSBBH-KAZBKCHUSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
I [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.46α = 90
b = 82.24β = 117.83
c = 91.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2008-01-15 
    • Deposition Author(s): Ku, S.Y.

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary