4L6A

Structure of human mitochondrial 5'(3')-deoxyribonucleotidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'(3')-deoxyribonucleotidase, mitochondrial
A
202Homo sapiensMutation(s): 0 
Gene Names: NT5M (DNT2)
EC: 3.1.3.-
Find proteins for Q9NPB1 (Homo sapiens)
Go to Gene View: NT5M
Go to UniProtKB:  Q9NPB1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.141 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.410α = 90.00
b = 73.410β = 90.00
c = 106.340γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references