4L57

High resolutin structure of human cytosolic 5'(3')-deoxyribonucleotidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors.

Pachl, P.Fabry, M.Rosenberg, I.Simak, O.Rezacova, P.Brynda, J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 461-470

  • DOI: 10.1107/S1399004713030502
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The human 5'(3')-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the struc ...

    The human 5'(3')-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.


    Organizational Affiliation

    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'(3')-deoxyribonucleotidase, cytosolic typeA, B195Homo sapiensMutation(s): 0 
Gene Names: DNT1NT5CUMPH2
EC: 3.1.3
Find proteins for Q8TCD5 (Homo sapiens)
Explore Q8TCD5 
Go to UniProtKB:  Q8TCD5
NIH Common Fund Data Resources
PHAROS  Q8TCD5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.128α = 68.16
b = 46.493β = 81.47
c = 61.409γ = 75.28
Software Package:
Software NamePurpose
SHELXrefinement
PDB_EXTRACTdata extraction
SHELXLrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Refinement description
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references