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- PDB-9c0p: M. tuberculosis PKS13 acyltransferase (AT) domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 9c0p
TitleM. tuberculosis PKS13 acyltransferase (AT) domain in complex with SuFEx inhibitor CEC215
ComponentsPolyketide synthase Pks13
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / polyketide synthase / acyltransferase / tuberculosis / inhibitor / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
sucrose / : / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKrieger, I.V. / Tang, S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-040487 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Welch FoundationA-0015 United States
CitationJournal: Nature / Year: 2025
Title: SuFEx-based antitubercular compound irreversibly inhibits Pks13.
Authors: Krieger, I.V. / Sukheja, P. / Yang, B. / Tang, S. / Selle, D. / Woods, A. / Engelhart, C. / Kumar, P. / Harbut, M.B. / Liu, D. / Tsuda, B. / Qin, B. / Bare, G.A.L. / Li, G. / Chi, V. / ...Authors: Krieger, I.V. / Sukheja, P. / Yang, B. / Tang, S. / Selle, D. / Woods, A. / Engelhart, C. / Kumar, P. / Harbut, M.B. / Liu, D. / Tsuda, B. / Qin, B. / Bare, G.A.L. / Li, G. / Chi, V. / Gambacurta, J. / Hvizdos, J. / Reagan, M. / Jones, I.L. / Massoudi, L.M. / Woolhiser, L.K. / Cascioferro, A. / Kundrick, E. / Singh, P. / Reiley, W. / Ioerger, T.R. / Kandula, D.R. / McCabe, J.W. / Guo, T. / Alland, D. / Boshoff, H.I. / Schnappinger, D. / Robertson, G.T. / Mdluli, K. / Lee, K.J. / Dong, J. / Li, S. / Schultz, P.G. / Joseph, S.B. / Love, M.S. / Sharpless, K.B. / Petrassi, H.M. / Chatterjee, A.K. / Sacchettini, J.C. / McNamara, C.W.
History
DepositionMay 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 13, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 3, 2025Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 1, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase Pks13
B: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,70124
Polymers111,0932
Non-polymers5,60822
Water9,224512
1
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,63314
Polymers55,5461
Non-polymers3,08613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,06910
Polymers55,5461
Non-polymers2,5229
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.665, 106.665, 258.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1377-

HOH

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Components

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Protein / Sugars , 2 types, 10 molecules AB

#1: Protein Polyketide synthase Pks13


Mass: 55546.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pks13, Rv3800c / Production host: Escherichia coli (E. coli)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 526 molecules

#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-A1ATV / N-{4-[(4-{[fluorodi(hydroxy)-lambda~4~-sulfanyl]oxy}phenoxy)methyl]phenyl}acetamide


Mass: 341.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16FNO5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH7.5, 1.8 M AmSO4, 4-6% PEG400

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.87→34.58 Å / Num. obs: 99712 / % possible obs: 95.9 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.045 / Net I/σ(I): 11.3
Reflection shellResolution: 1.873→2.027 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.484 / Num. unique obs: 4987 / CC1/2: 0.654 / % possible all: 68.5

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Processing

Software
NameClassification
PDB-REDOrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→34.58 Å / SU B: 6.357 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19795 5023 5 %RANDOM
Rwork0.1717 ---
obs0.17304 94682 80.88 %-
Displacement parametersBiso mean: 24.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.87→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7110 0 325 512 7947

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