4KPC

Crystal structure of the nucleoside diphosphate kinase b from Leishmania braziliensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.175 

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
  • Primary Citation of Related Structures:  
    4KPC

  • 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 make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions ...

    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

    Avenida Bandeirantes, 3900, Monte Alegre, Zip Code 14040-901, Ribeirão Preto, SP, Brazil. arthurdeoliveira@ffclrp.usp.br.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase bA, B171Leishmania braziliensisMutation(s): 0 
Gene Names: LBRM_32_3210
EC: 2.7.4.6
UniProt
Find proteins for A4HKT8 (Leishmania braziliensis)
Explore A4HKT8 
Go to UniProtKB:  A4HKT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4HKT8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.175 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.284α = 90
b = 110.284β = 90
c = 110.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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