1BHN

NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina.

Ladner, J.E.Abdulaev, N.G.Kakuev, D.L.Tordova, M.Ridge, K.D.Gilliland, G.L.

(1999) Acta Crystallogr.,Sect.D 55: 1127-1135


  • PubMed Abstract: 
  • The crystal structures of two isoforms of nucleoside diphosphate kinase from bovine retina overexpressed in Escherischia coli have been determined to 2.4 A resolution. Both the isoforms, NBR-A and NBR-B, are hexameric and the fold of the monomer is i ...

    The crystal structures of two isoforms of nucleoside diphosphate kinase from bovine retina overexpressed in Escherischia coli have been determined to 2.4 A resolution. Both the isoforms, NBR-A and NBR-B, are hexameric and the fold of the monomer is in agreement with NDP-kinase structures from other biological sources. Although the polypeptide chains of the two isoforms differ by only two residues, they crystallize in different space groups. NBR-A crystallizes in space group P212121 with an entire hexamer in the asymmetric unit, while NBR-B crystallizes in space group P43212 with a trimer in the asymmetric unit. The highly conserved nucleotide-binding site observed in other nucleoside diphosphate kinase structures is also observed here. Both NBR-A and NBR-B were crystallized in the presence of cGMP. The nucleotide is bound with the base in the anti conformation. The NBR-A active site contained both cGMP and GDP each bound at half occupancy. Presumably, NBR-A had retained GDP (or GTP) from the purification process. The NBR-B active site contained only cGMP.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, National Institute of Standards and Technology and the University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE TRANSFERASE
A, B, C, D, E, F
152Bos taurusGene Names: NME1-1
EC: 2.7.4.6
Find proteins for P52174 (Bos taurus)
Go to UniProtKB:  P52174
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
35G
Query on 35G

Download SDF File 
Download CCD File 
A, B, C, D, E, F
GUANOSINE-3',5'-MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.880α = 90.00
b = 92.110β = 90.00
c = 131.630γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
XENGENdata scaling
AMoREphasing
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance