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- PDB-8cov: Pa.FabF-C164Q in complex with 6-chloro-2-methyl-1H-indole-5-carbo... -

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Basic information

Entry
Database: PDB / ID: 8cov
TitlePa.FabF-C164Q in complex with 6-chloro-2-methyl-1H-indole-5-carboxylic acid
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / FabF / Pseudomonas aeruginosa / inhibitor / complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / 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 ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / 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
Similarity search - Domain/homology
FORMIC ACID / PHOSPHATE ION / Chem-VBR / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGeorgiou, C. / Brenk, R. / Espeland, L.O.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway273588 Norway
Citation
Journal: Eur.J.Med.Chem. / Year: 2025
Title: Towards new antibiotics: P. aeruginosa FabF ligands discovered by crystallographic fragment screening followed by hit expansion.
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhins'ky, V. / Haug, B.E. / Mainkar, P.S. / Brenk, R.
#1: Journal: Chemrxiv / Year: 2023
Title: New starting points for antibiotics targeting P. aeruginosa FabF discovered by crystallographic fragment screening followed by hit expansion
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhinsky, V. / Haug, B.E. / Mainkar, P. / Brenk, R.
History
DepositionFeb 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2May 7, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,29131
Polymers86,6452
Non-polymers2,64529
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-15 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.392, 65.344, 84.223
Angle α, β, γ (deg.)90.00, 102.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 413 / Label seq-ID: 1 - 412

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 43322.715 Da / Num. of mol.: 2 / Mutation: C164Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabF1, PA2965 / Production host: Escherichia coli (E. coli)
References: UniProt: G3XDA2, beta-ketoacyl-[acyl-carrier-protein] synthase II

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Non-polymers , 5 types, 453 molecules

#2: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-VBR / 6-chloranyl-2-methyl-1~{H}-indole-5-carboxylic acid


Mass: 209.629 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.22 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.20M ammonium formate and 31.2% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 1.8→82.29 Å / Num. obs: 68897 / % possible obs: 98.1 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.4
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 21137 / CC1/2: 0.797 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→51.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.098 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19523 3454 5 %RANDOM
Rwork0.168 ---
obs0.16938 65440 97.85 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.768 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å21.26 Å2
2---0.46 Å20 Å2
3----1.91 Å2
Refinement stepCycle: 1 / Resolution: 1.8→51.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 146 424 6644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136413
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176113
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.638677
X-RAY DIFFRACTIONr_angle_other_deg1.371.57414002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40620.491326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.531151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9831559
X-RAY DIFFRACTIONr_chiral_restr0.0670.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021502
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9572.5413337
X-RAY DIFFRACTIONr_mcbond_other1.9562.543336
X-RAY DIFFRACTIONr_mcangle_it2.6423.8034180
X-RAY DIFFRACTIONr_mcangle_other2.6423.8044181
X-RAY DIFFRACTIONr_scbond_it3.2113.0523076
X-RAY DIFFRACTIONr_scbond_other3.2113.0533077
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6654.44484
X-RAY DIFFRACTIONr_long_range_B_refined5.98231.6917134
X-RAY DIFFRACTIONr_long_range_B_other5.9831.4987064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13110 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 245 -
Rwork0.277 4756 -
obs--96.47 %

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