3OTX

Crystal Structure of Trypanosoma brucei rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A

• PDB DOI: https://doi.org/10.2210/pdb3OTX/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-09-14 Released: 2011-06-29 
• Deposition Author(s): Kuettel, S., Greenwald, J., Kostrewa, D., Ahmed, S., Scapozza, L., Perozzo, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.214 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Crystal Structures of T. b. rhodesiense Adenosine Kinase Complexed with Inhibitor and Activator: Implications for Catalysis and Hyperactivation

Kuettel, S., Greenwald, J., Kostrewa, D., Ahmed, S., Scapozza, L., Perozzo, R.

(2011) PLoS Negl Trop Dis 5: e1164-e1164

• PubMed: 21629723 
• DOI: https://doi.org/10.1371/journal.pntd.0001164
• Primary Citation of Related Structures:  
  2XTB, 3OTX


• PubMed Abstract: 
  

  The essential purine salvage pathway of Trypanosoma brucei bears interesting catalytic enzymes for chemotherapeutic intervention of Human African Trypanosomiasis. Unlike mammalian cells, trypanosomes lack de novo purine synthesis and completely rely on salvage from their hosts. One of the key enzymes is adenosine kinase which catalyzes the phosphorylation of ingested adenosine to form adenosine monophosphate (AMP) utilizing adenosine triphosphate (ATP) as the preferred phosphoryl donor.

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Organizational Affiliation: 

Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Lausanne, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.14 kDa 
• Atom Count: 6,061 
• Modelled Residue Count: 680 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine kinase, putative	A, B	347	Trypanosoma brucei	Mutation(s): 1  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP5	C [auth A], E [auth B]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C20 H29 N10 O22 P5 OIMACDRJUANHTJ-XPWFQUROSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AP5	Binding MOAD:  3OTX	IC50: 2.94e+4 (nM) from 1 assay(s)
	PDBBind:  3OTX	IC50: 2.94e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.214 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.893	α = 90
b = 70.549	β = 90.77
c = 72.41	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Kuettel, S., Greenwald, J., Kostrewa, D., Ahmed, S., Scapozza, L., Perozzo, R.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description