5L50

Crystal structure of enzyme in purine metabolism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Oligomeric interface modulation causes misregulation of purine 5 -nucleotidase in relapsed leukemia.

Hnizda, A.Skerlova, J.Fabry, M.Pachl, P.Sinalova, M.Vrzal, L.Man, P.Novak, P.Rezacova, P.Veverka, V.

(2016) BMC Biol 14: 91-91

  • DOI: https://doi.org/10.1186/s12915-016-0313-y
  • Primary Citation of Related Structures:  
    5K7Y, 5L4Z, 5L50

  • PubMed Abstract: 

    Relapsed acute lymphoblastic leukemia (ALL) is one of the main causes of mortality in childhood malignancies. Previous genetic studies demonstrated that chemoresistant ALL is driven by activating mutations in NT5C2, the gene encoding cytosolic 5´-nucleotidase (cN-II). However, molecular mechanisms underlying this hyperactivation are still unknown. Here, we present kinetic and structural properties of cN-II variants that represent 75 % of mutated alleles in patients who experience relapsed ALL (R367Q, R238W and L375F).


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic. hnizda@uochb.cas.cz.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosolic purine 5'-nucleotidase555Homo sapiensMutation(s): 1 
Gene Names: NT5C2NT5BNT5CPPNT5
EC: 3.1.3.5
UniProt & NIH Common Fund Data Resources
Find proteins for P49902 (Homo sapiens)
Explore P49902 
Go to UniProtKB:  P49902
PHAROS:  P49902
GTEx:  ENSG00000076685 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49902
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.356α = 90
b = 125.988β = 90
c = 130.781γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic15-06582S

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description