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)

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 5MYP

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

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q583M9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-04-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.