4KPC

Crystal structure of the nucleoside diphosphate kinase b from Leishmania braziliensis

PDB DOI: https://doi.org/10.2210/pdb4KPC/pdb

Classification: TRANSFERASE
Organism(s): Leishmania braziliensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-13 Released: 2014-07-09
Deposition Author(s): Vieira, P.S., Giuseppe, P.O., Santos, C.R., Cunha, E.M.F., de Oliveira, A.H.C., Murakami, M.T.

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 1.2 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

PubMed: 25643978 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 37.95 kDa
Atom Count: 2,236
Modelled Residue Count: 279
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase b	A, B	171	Leishmania braziliensis	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4HKT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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 = 110.284	α = 90
b = 110.284	β = 90
c = 110.284	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

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
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations