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 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 2.0 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

  • DOI: https://doi.org/10.1016/s0969-2126(98)00020-3
  • Primary Citation of Related Structures:  
    1RKD

  • 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 previously unknown structure ...

    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: 
    • 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
    • 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
    Organizational Affiliation: 

    Department of Molecular Biology, Uppsala University, Sweden.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOKINASEA309Escherichia coli K-12Mutation(s): 0 
Gene Names: rbsK, b3752, JW3731
EC: 2.7.1.15
UniProt
Find proteins for P0A9J6 (Escherichia coli (strain K12))
Explore P0A9J6 
Go to UniProtKB:  P0A9J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9J6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
RIB
Query on RIB
Download Ideal Coordinates CCD File 
B [auth A]alpha-D-ribofuranose
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 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 
  • R-Value Observed: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.4α = 90
b = 95.4β = 90
c = 154.87γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary