4FKX | pdb_00004fkx

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

PDB DOI: https://doi.org/10.2210/pdb4FKX/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: 1.70 Å
R-Value Free:
0.182 (Depositor), 0.190 (DCC)
R-Value Work:
0.152 (Depositor), 0.161 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 55.13 kDa
Atom Count: 4,210
Modeled Residue Count: 458
Deposited Residue Count: 483
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q381H3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDP Query on CDP Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth C] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth C] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], I [auth C]	CYTIDINE-5'-DIPHOSPHATE C₉ H₁₅ N₃ O₁₁ P₂ ZWIADYZPOWUWEW-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain I [auth C]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	E [auth A], G [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.182 (Depositor), 0.190 (DCC)
R-Value Work: 0.152 (Depositor), 0.161 (DCC)
R-Value Observed: 0.154 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.63	α = 90
b = 121.37	β = 90
c = 112.87	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-06-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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

4FKX | pdb_00004fkx

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

Literature

Structural and Functional Analyses of Trypanosoma brucei Nucleoside Diphosphate Kinase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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