5MYP | pdb_00005myp

Structure of apo-TbALDH3

• PDB DOI: https://doi.org/10.2210/pdb5MYP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-27 Released: 2017-04-19 
• Deposition Author(s): Zoltner, M., Zhang, N., Horn, D., Field, M.C.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: in silico

Literature

Activation of an anti-trypanosomal benzoxaborole requires both host and parasite factors

Zhang, N., Zoltner, M., Leung, K.F., Scullion, P., Hutchinson, S., Canavate del Pino, R., Barrett, M., Freud, Y., Alley, D., Read, K., Horn, D., Field, M.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 120.14 kDa 
• Atom Count: 8,406 
• Modeled Residue Count: 970 
• Deposited Residue Count: 1,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase	A, B	546	Trypanosoma brucei	Mutation(s): 0  Gene Names: Tb427.06.3050
UniProt
Find proteins for Q583M9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q583M9  Go to UniProtKB:  Q583M9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.717	α = 90
b = 63.95	β = 98.64
c = 91.746	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Zoltner, M., Zhang, N., Horn, D., Field, M.C.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/L018853/1

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description