9C9O | pdb_00009c9o

M. tuberculosis PKS13 acyltransferase (AT) domain in complex with SuFEx inhibitor CMX410 - reaction product

PDB DOI: https://doi.org/10.2210/pdb9C9O/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-14 Released: 2025-05-07
Deposition Author(s): Krieger, I.V., Tang, S., Sacchetini, J.C., TB Structural Genomics Consortium (TBSGC)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation, Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.231 (Depositor), 0.232 (DCC)
R-Value Work:
0.194 (Depositor), 0.196 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A SuFEx-based TB clinical candidate irreversibly inhibits Pks13

Krieger, I.V., Sacchetini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 170.35 kDa
Atom Count: 7,875
Modeled Residue Count: 946
Deposited Residue Count: 1,536
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase Pks13	A	512	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pks13, Rv3800c EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X8D2 Go to UniProtKB: I6X8D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6X8D2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase Pks13	B, C	512	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pks13, Rv3800c EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X8D2 Go to UniProtKB: I6X8D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6X8D2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	D, E, F, G, H D, E, F, G, H, I, J	2		N/A	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AVL (Subject of Investigation/LOI) Query on A1AVL Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	4-({2,6-difluoro-4-[3-(methanesulfonamido)-1H-1,2,4-triazol-1-yl]phenyl}methoxy)phenyl hydrogen sulfate C₁₆ H₁₄ F₂ N₄ O₇ S₂ OBVUSHOELYWBEI-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	M [auth A], N [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	K [auth A], L [auth A], P [auth B], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	D, E, F, G, H D, E, F, G, H, I, J	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.231 (Depositor), 0.232 (DCC)
R-Value Work: 0.194 (Depositor), 0.196 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.673	α = 90
b = 106.673	β = 90
c = 258.74	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Krieger, I.V.

Tang, S.

Sacchetini, J.C.

TB Structural Genomics Consortium (TBSGC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01AI095208
Bill & Melinda Gates Foundation	United States	INV-040487
Welch Foundation	United States	A-0015