8OQM

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-10

PDB DOI: https://doi.org/10.2210/pdb8OQM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-04-12 Released: 2024-01-24
Deposition Author(s): Dalwani, S., Wierenga, R.K., Venkatesan, R.
Funding Organization(s): Academy of Finland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.242
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate channeling path between them

Dalwani, S., Metz, A., Huschmann, F.U., Weiss, M.S., Wierenga, R.K., Venkatesan, R.

(2024) Biorxiv

DOI: https://doi.org/10.1101/2024.01.11.575214

Macromolecule Content

Total Structure Weight: 243.84 kDa
Atom Count: 16,883
Modelled Residue Count: 2,250
Deposited Residue Count: 2,278
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyacyl-CoA dehydrogenase	A, B	736	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: fadB, Rv0860 EC: 1.1.1.35
UniProt
Find proteins for O53872 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53872 Go to UniProtKB: O53872
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O53872
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acyltransferase Rv0859	C, D	403	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: fadA, Rv0859 EC: 2.3.1
UniProt
Find proteins for O53871 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53871 Go to UniProtKB: O53871
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O53871
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VWO (Subject of Investigation/LOI) Query on VWO Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B]	DA [auth D], J [auth A], R [auth B]	6-azanyl-4-oxidanyl-naphthalene-2-sulfonic acid C₁₀ H₉ N O₄ S HBZVNWNSRNTWPS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain DA [auth D] Focus chain J [auth A] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] E [auth A] F [auth A] AA [auth D], BA [auth D], CA [auth D], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B]	G [auth A], H [auth A], I [auth A], N [auth B], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth B]