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- PDB-9pl0: The structure of the Fusobacterium nucleatum Enoyl-Acyl Carrier P... -

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Basic information

Entry
Database: PDB / ID: 9pl0
TitleThe structure of the Fusobacterium nucleatum Enoyl-Acyl Carrier Protein Reductase (FabK) bound to an inhibitor
ComponentsEnoyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / FabK / Fusobacterium nucleatum / Enoyl-Acyl Carrier Protein Reductase / FAS-II pathway
Function / homology
Function and homology information


nitronate monooxygenase activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / oxidoreductase activity
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / CITRIC ACID / FLAVIN MONONUCLEOTIDE / Chem-JEF / Enoyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAlaidi, O. / Avad, K. / Hevener, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)1R21DE032798 United States
CitationJournal: Acs Bio Med Chem Au / Year: 2025
Title: Structural and Biochemical Characterization of Fusobacterium nucleatum Enoyl-ACP Reductase II (FabK) Reveals the Basis for Bacterial Species-Specific Inhibition
Authors: Avad, K. / Alaidi, O. / Okpomo, D. / Pavel, F.B.A. / Doran, D. / Matheson, M. / Sun, D. / Hurdle, J. / Hevener, K.E.
History
DepositionJul 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase
B: Enoyl-[acyl-carrier-protein] reductase
C: Enoyl-[acyl-carrier-protein] reductase
D: Enoyl-[acyl-carrier-protein] reductase
E: Enoyl-[acyl-carrier-protein] reductase
F: Enoyl-[acyl-carrier-protein] reductase
J: Enoyl-[acyl-carrier-protein] reductase
G: Enoyl-[acyl-carrier-protein] reductase
H: Enoyl-[acyl-carrier-protein] reductase
I: Enoyl-[acyl-carrier-protein] reductase
K: Enoyl-[acyl-carrier-protein] reductase
L: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,36190
Polymers434,60512
Non-polymers22,75778
Water15,997888
1
A: Enoyl-[acyl-carrier-protein] reductase
B: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,97916
Polymers72,4342
Non-polymers4,54514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-67 kcal/mol
Surface area22680 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase
D: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,65117
Polymers72,4342
Non-polymers4,21715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-66 kcal/mol
Surface area23170 Å2
MethodPISA
3
E: Enoyl-[acyl-carrier-protein] reductase
F: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,05717
Polymers72,4342
Non-polymers4,62315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-58 kcal/mol
Surface area22500 Å2
MethodPISA
4
J: Enoyl-[acyl-carrier-protein] reductase
I: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,86115
Polymers72,4342
Non-polymers3,42713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-51 kcal/mol
Surface area22910 Å2
MethodPISA
5
G: Enoyl-[acyl-carrier-protein] reductase
H: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,70513
Polymers72,4342
Non-polymers3,27111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-60 kcal/mol
Surface area22860 Å2
MethodPISA
6
K: Enoyl-[acyl-carrier-protein] reductase
L: Enoyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,10712
Polymers72,4342
Non-polymers2,67310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-56 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.272, 194.081, 166.818
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 12 molecules ABCDEFJGHIKL

#1: Protein
Enoyl-[acyl-carrier-protein] reductase


Mass: 36217.078 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: FN0174 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RGV3, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 7 types, 966 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-A1CIO / N-{[4-(4-bromophenyl)-1H-imidazol-2-yl]methyl}-N'-[6-(trifluoromethyl)-1,3-benzothiazol-2-yl]urea


Mass: 496.304 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C19H13BrF3N5OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C30H63NO10
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% Jeffamine ED-2001 pH 7.0, 0.1M Sodium Citrate Tribasic pH 5.0, 8.3 uMolar of the inhibitor (final DMSO concentration 0.2 %).
Temp details: Cryoprotection using a 70% sucrose solution, the crystals were briefly socked with 10mM solution of inhibitor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 26, 2024
RadiationMonochromator: Double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.25→52.27 Å / Num. obs: 156928 / % possible obs: 99.59 % / Redundancy: 7.1 % / Biso Wilson estimate: 33.09 Å2 / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.3685 / Rpim(I) all: 0.1492 / Rrim(I) all: 0.3979 / Net I/σ(I): 3.73
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 7.2 % / Rmerge(I) obs: 2.09 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 11137 / CC1/2: 0.492 / CC star: 0.812 / Rpim(I) all: 0.8358 / Rrim(I) all: 2.252 / % possible all: 98.51

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALS3.8data reduction
PHASER2.8.3phasing
Coot0.9.8.95model building
DIALS3.8data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→52.27 Å / SU ML: 0.3289 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.1912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2536 1985 1.27 %
Rwork0.2134 154308 -
obs0.2139 156293 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.04 Å2
Refinement stepCycle: LAST / Resolution: 2.25→52.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28116 0 975 888 29979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003429494
X-RAY DIFFRACTIONf_angle_d0.601239765
X-RAY DIFFRACTIONf_chiral_restr0.04224623
X-RAY DIFFRACTIONf_plane_restr0.00545020
X-RAY DIFFRACTIONf_dihedral_angle_d15.74611133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.37081380.303310833X-RAY DIFFRACTION98.51
2.31-2.370.31571460.273910973X-RAY DIFFRACTION98.79
2.37-2.440.31051360.263810832X-RAY DIFFRACTION98.88
2.44-2.520.30841440.263911005X-RAY DIFFRACTION99.29
2.52-2.610.31671440.252411088X-RAY DIFFRACTION99.8
2.61-2.710.30461360.249110947X-RAY DIFFRACTION99.9
2.71-2.830.29461420.233911046X-RAY DIFFRACTION99.88
2.83-2.980.25541410.222611033X-RAY DIFFRACTION99.93
2.98-3.170.25271390.208711056X-RAY DIFFRACTION99.91
3.17-3.420.24371450.201111097X-RAY DIFFRACTION99.99
3.42-3.760.21641440.188111059X-RAY DIFFRACTION99.95
3.76-4.30.22861420.173311094X-RAY DIFFRACTION99.99
4.3-5.420.21951490.181811081X-RAY DIFFRACTION99.93
5.42-52.270.21971390.216511164X-RAY DIFFRACTION99.59

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