4FKY

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

• PDB DOI: https://doi.org/10.2210/pdb4FKY/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-13 Released: 2012-06-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.188 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 

Starting Model: experimental

Literature

Crystal structure of nucleoside diphosphate kinase B from Trypanosma brucei bound to GTP

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.25 kDa 
• Atom Count: 4,202 
• Modelled Residue Count: 457 
• Deposited Residue Count: 483 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B, C	161	Trypanosoma brucei brucei TREU927	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], F [auth B], I [auth C]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MPD	H [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG	E [auth A], G [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.188 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M34FKY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.68	α = 90
b = 121.49	β = 90
c = 112.83	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

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