4N09

Structure of Trypanosoma brucei brucei adenosine kinase in complex with adenosine and AMPPNP

PDB DOI: https://doi.org/10.2210/pdb4N09/pdb

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

Deposited: 2013-10-01 Released: 2014-01-15
Deposition Author(s): Timm, J., Gonzalez-Pacanowska, D., Wilson, K.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.221
R-Value Work: 0.186
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structures of adenosine kinase from Trypanosoma brucei brucei.

Timm, J., Gonzalez-Pacanowska, D., Wilson, K.S.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 34-39

PubMed: 24419613 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X13033621
Primary Citation of Related Structures:
4N08, 4N09

PubMed Abstract:
Trypanosoma brucei is a single-cellular parasite of the genus Kinetoplastida and is the causative agent of African sleeping sickness in humans. Adenosine kinase is a key enzyme in the purine-salvage pathway, phosphorylating adenosine to AMP, and also activates cytotoxic analogues such as cordycepin and Ara-A by their phosphorylation. The structures of T. brucei brucei adenosine kinase (TbAK) in its unliganded open conformation and complexed with adenosine and ADP in the closed conformation are both reported to 2.6 Å resolution. The structures give insight into the binding mode of the substrates and the conformational change induced upon substrate binding. This information can be used to guide the improvement of cytotoxic substrate analogues as potential antitrypanosomal drugs.

Organizational Affiliation

Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England.

Macromolecule Content

Total Structure Weight: 155.82 kDa
Atom Count: 10,616
Modelled Residue Count: 1,377
Deposited Residue Count: 1,392
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine kinase	A, B, C, D	348	Trypanosoma brucei brucei TREU927	Mutation(s): 0 Gene Names: Tb927.6.2360 EC: 2.7.1.20
UniProt
Find proteins for Q584S0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q584S0 Go to UniProtKB: Q584S0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q584S0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D]	F [auth A], I [auth B], L [auth C], N [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]
ADN Query on ADN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D]	E [auth A], H [auth B], K [auth C], M [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B]	G [auth A], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]