4FKX

Crystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to CDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to CDP

Gardberg, A.S.Edwards, T.E.Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase
A, B, C
161Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb11.01.7800
EC: 2.7.4.6
UniProt
Find proteins for Q381H3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q381H3 
Go to UniProtKB:  Q381H3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ381H3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDP
Query on CDP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
I [auth C]
CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
H [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.63α = 90
b = 121.37β = 90
c = 112.87γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description