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- PDB-9ifz: FSP1 (tetrapod ancestor) bound to FAD -

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Basic information

Entry
Database: PDB / ID: 9ifz
TitleFSP1 (tetrapod ancestor) bound to FAD
ComponentsFSP1 (Tetrapod ancestor)
KeywordsOXIDOREDUCTASE / Flavin / NAD / coenzyme Q / ferroptosis / myristoylation / inhibitor discovery
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMammalia (mammals)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCecchini, D. / Mattevi, A.
Funding supportEuropean Union, Italy, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101094471European Union
Italian Association for Cancer Research28754 Italy
CitationJournal: To Be Published
Title: Best-in-Class FSP1 Inhibitors Unraveled By AI-Enhanced Adaptive Screening Platform
Authors: Cecchini, D. / Mattevi, A.
History
DepositionFeb 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 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: FSP1 (Tetrapod ancestor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9145
Polymers39,8111
Non-polymers1,1044
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint1 kcal/mol
Surface area15280 Å2
Unit cell
Length a, b, c (Å)43.092, 81.512, 57.685
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FSP1 (Tetrapod ancestor)


Mass: 39810.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalia (mammals) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.06 M MgCl2, 0.06 M CaCl2, 0.1 M HEPES/MOPS (acid) pH 7.5; 20% v/v PEG500*MME, 10% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.1→81.51 Å / Num. obs: 23156 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.086 / Rrim(I) all: 0.227 / Χ2: 1.01 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.062 / Num. measured all: 13548 / Num. unique obs: 1912 / CC1/2: 0.702 / Rpim(I) all: 0.428 / Rrim(I) all: 1.146 / Χ2: 1 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.449 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22744 1137 4.9 %RANDOM
Rwork0.18029 ---
obs0.1827 21994 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.449 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-1.52 Å2
2--0.03 Å2-0 Å2
3---0.8 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 74 118 2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122893
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162795
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.6383908
X-RAY DIFFRACTIONr_angle_other_deg0.4651.5756447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.02358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25310501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
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_it2.1792.4891459
X-RAY DIFFRACTIONr_mcbond_other2.1782.4891459
X-RAY DIFFRACTIONr_mcangle_it3.4114.4591822
X-RAY DIFFRACTIONr_mcangle_other3.414.4621823
X-RAY DIFFRACTIONr_scbond_it3.2272.9441434
X-RAY DIFFRACTIONr_scbond_other3.2262.9461435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1875.22087
X-RAY DIFFRACTIONr_long_range_B_refined6.75526.823262
X-RAY DIFFRACTIONr_long_range_B_other6.71726.623253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 82 -
Rwork0.238 1644 -
obs--99.71 %

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