8OWQ

Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP and 2-(1-(3,4-dihydroxyphenyl)-5-phenyl-1H-indol-3-yl)-2-oxoacetic acid

PDB DOI: https://doi.org/10.2210/pdb8OWQ/pdb

Classification: LIGASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-04-28 Released: 2024-05-08
Deposition Author(s): Mendes, V., Blundell, T.L.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.256
R-Value Work: 0.207
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Development of new inhibitors against M. tuberculosis CoaBC using a fragment based approach.

Hess, J., Mendes, V., Evans, J.C., Trapero, A., Marchetti, C., Blaszczyk, M., Bryant, O., Spry, C., Coyne, A.G., Boshoff, H.I.M., Barry, C.E., Mizrahi, V., Blundell, T.L., Abell, C.

To be published.

Macromolecule Content

Total Structure Weight: 103.43 kDa
Atom Count: 6,840
Modelled Residue Count: 854
Deposited Residue Count: 948
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme A biosynthesis bifunctional protein CoaBC	A, B, C, D	237	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: coaBC, MSMEG_3054 EC: 4.1.1.36 (PDB Primary Data), 6.3.2.5 (PDB Primary Data)
UniProt
Find proteins for A0QWT2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QWT2 Go to UniProtKB: A0QWT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QWT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP Query on CTP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	E [auth A], J [auth B], M [auth C], Q [auth D]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D]
W4X (Subject of Investigation/LOI) Query on W4X 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 L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C]	G [auth A] H [auth A] I [auth A] L [auth B] O [auth C] G [auth A], H [auth A], I [auth A], L [auth B], O [auth C], P [auth C]	2-[1-[3,4-bis(oxidanyl)phenyl]-5-phenyl-indol-3-yl]-2-oxidanylidene-ethanoic acid C₂₂ H₁₅ N O₅ WKTMYKMXGIXMJJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A], K [auth B], N [auth C], R [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D]