4FKY | pdb_00004fky

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Analyses of Trypanosoma brucei Nucleoside Diphosphate Kinase

Makori, P., Boeckman, M.P., David, H.S., Payne, F., Gatling, M., Greer, C., Hayes, D., Jefferson, A., Maxwell, M., Smith, C., Watson, J., Williams, L., Barkley, J., Pepper, C., Zininga, T., Subramanian, S., Abramov, A., Gardberg, A.S., Edwards, T.E., Staker, B.L., Stewart, L.J., Myler, P.J., Asojo, O.A., Jeje, O., Fanucchi, S., Achilonu, I., Smith, C.L., Chakafana, G.

(2026) ACS Omega 

• DOI: https://doi.org/10.1021/acsomega.5c11614

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 
• Modeled 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 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34FKY

Space Group: C 2 2 2₁

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
• Version 1.2: 2026-03-18
  Changes: Database references, Structure summary