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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA, B420Arabidopsis thalianaMutation(s): 0 
Gene Names: F10F5.1MTKAt1g49820
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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
 Ligand Interaction
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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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2007-05-16 
  • 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