1RKD

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.

Sigrell, J.A.Cameron, A.D.Jones, T.A.Mowbray, S.L.

(1998) Structure 6: 183-193

  • Also Cited By: 1GQT

  • PubMed Abstract: 
  • D-ribose must be phosphorylated at O5' before it can be used in either anabolism or catabolism. This reaction is catalysed by ribokinase and requires the presence of ATP and magnesium. Ribokinase is a member of a family of carbohydrate kinases of pre ...

    D-ribose must be phosphorylated at O5' before it can be used in either anabolism or catabolism. This reaction is catalysed by ribokinase and requires the presence of ATP and magnesium. Ribokinase is a member of a family of carbohydrate kinases of previously unknown structure.


    Related Citations: 
    • Ribokinase from Escherichia Coli K12. Nucleotide Sequence and Overexpression of the Rbsk Gene and Purification of Ribokinase
      Hope, J.N.,Bell, A.W.,Hermodson, M.A.,Groarke, J.M.
      (1986) J.Biol.Chem. 261: 7663
    • Purification, Characterization, and Crystallization of Escherichia Coli Ribokinase
      Sigrell, J.A.,Cameron, A.D.,Jones, T.A.,Mowbray, S.L.
      (1997) Protein Sci. 6: 2474


    Organizational Affiliation

    Department of Molecular Biology, Uppsala University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOKINASE
A
309Escherichia coli (strain K12)Gene Names: rbsK
EC: 2.7.1.15
Find proteins for P0A9J6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9J6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
RIB
Query on RIB

Download SDF File 
Download CCD File 
A
RIBOSE
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 95.400α = 90.00
b = 95.400β = 90.00
c = 154.870γ = 120.00
Software Package:
Software NamePurpose
MLPHAREphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance