4KPC

Crystal structure of the nucleoside diphosphate kinase b from Leishmania braziliensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and biophysical characterization of the nucleoside diphosphate kinase from Leishmania braziliensis.

Vieira, P.S.de Giuseppe, P.O.Murakami, M.T.de Oliveira, A.H.

(2015) Bmc Struct.Biol. 15: 2-2

  • DOI: 10.1186/s12900-015-0030-8

  • PubMed Abstract: 
  • Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. It is also secreted by the intracellular parasite Leishmania to modulate the host response. These functions ...

    Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. It is also secreted by the intracellular parasite Leishmania to modulate the host response. These functions make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions.


    Organizational Affiliation

    Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil. plinio.vieira@lnbio.cnpem.br.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoside diphosphate kinase b
A, B
171Leishmania braziliensisMutation(s): 0 
EC: 2.7.4.6
Find proteins for A4HKT8 (Leishmania braziliensis)
Go to UniProtKB:  A4HKT8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.170 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 110.284α = 90.00
b = 110.284β = 90.00
c = 110.284γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2015-06-17
    Type: Database references