8OWP | pdb_00008owp

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

PDB DOI: https://doi.org/10.2210/pdb8OWP/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: 1.99 Å
R-Value Free:
0.254 (Depositor), 0.247 (DCC)
R-Value Work:
0.199 (Depositor), 0.197 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8OWP

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: 102.32 kDa
Atom Count: 6,533
Modeled Residue Count: 848
Deposited Residue Count: 948
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QWT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 I [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	E [auth A], I [auth B], K [auth C], O [auth D]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D]
W52 (Subject of Investigation/LOI) Query on W52 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth C]	G [auth A], H [auth A], M [auth C]	2-[1-(4-hydroxyphenyl)-5-phenyl-indol-3-yl]-2-oxidanylidene-ethanoic acid C₂₂ H₁₅ N O₄ JLROENQELDGFNR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	F [auth A], J [auth B], L [auth C], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.254 (Depositor), 0.247 (DCC)
R-Value Work: 0.199 (Depositor), 0.197 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.816	α = 90
b = 76.409	β = 90
c = 143.193	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1158806
Bill & Melinda Gates Foundation	United States	OPP1024021

Revision History (Full details and data files)

Version 1.0: 2024-05-08
Type: Initial release

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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.