9C1D | pdb_00009c1d

Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO

PDB DOI: https://doi.org/10.2210/pdb9C1D/pdb

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

Deposited: 2024-05-29 Released: 2025-05-21
Deposition Author(s): Tang, S., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Welch Foundation, Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 ?
R-Value Free:
0.221 (Depositor), 0.221 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO

Tang, S., Sacchettini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 164.14 kDa
Atom Count: 8,056
Modeled Residue Count: 948
Deposited Residue Count: 1,473
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase Pks13	A, B, C	491	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

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE5 Query on PE5 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C₁₈ H₃₈ O₉ CUDPPTPIUWYGFI-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain NA [auth B] MOL2 format, chain NA [auth B] mmCIF format, chain NA [auth B]	NA [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain NA [auth B] Interactions & Density Focus chain NA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain P [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain P [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain P [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	BA [auth A] CB [auth B] DA [auth A] P [auth A] T [auth A] BA [auth A], CB [auth B], DA [auth A], P [auth A], T [auth A], TA [auth B], X [auth A], XA [auth B], Y [auth A], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain P [auth A] Focus chain T [auth A] Focus chain TA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain P [auth A] Focus chain T [auth A] Focus chain TA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HB [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] HB [auth C] E [auth A], F [auth A], G [auth A], H [auth A], HB [auth C], I [auth A], J [auth A], JA [auth B], KA [auth B], LA [auth B], MA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HB [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HB [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain AA [auth A]	AA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain U [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain D [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain D [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain D [auth A]	D [auth A] PA [auth B] RA [auth B] S [auth A] SA [auth B] D [auth A], PA [auth B], RA [auth B], S [auth A], SA [auth B], U [auth A], VA [auth B], WA [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain U [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Interactions & Density Focus chain D [auth A] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain U [auth A] Focus chain VA [auth B] Focus chain WA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain DB [auth B] SDF format, chain EA [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B]	AB [auth B] BB [auth B] CA [auth A] DB [auth B] EA [auth A] AB [auth B], BB [auth B], CA [auth A], DB [auth B], EA [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth B], Q [auth A], QA [auth B], R [auth A], UA [auth B], V [auth A], W [auth A], YA [auth B], ZA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EB [auth B] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain HA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain HA [auth A]	EB [auth B] FA [auth A] FB [auth B] GA [auth A] GB [auth B] EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], HA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Interactions & Density Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain IA [auth A] MOL2 format, chain IA [auth A] mmCIF format, chain IA [auth A]	IA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain IA [auth A] Interactions & Density Focus chain IA [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 ?
R-Value Free: 0.221 (Depositor), 0.221 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 106.183	α = 90
b = 106.183	β = 90
c = 259.679	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Tang, S.

Sacchettini, 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
Welch Foundation	United States	A-0015
Bill & Melinda Gates Foundation	United States	INV-040487