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- PDB-9szx: Human fumarylacetoacetate hydrolase (FAH) in complex with 3C9 -

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Basic information

Entry
Database: PDB / ID: 9szx
TitleHuman fumarylacetoacetate hydrolase (FAH) in complex with 3C9
ComponentsFumarylacetoacetase
KeywordsHYDROLASE / Human fumarylacetoacetate hydrolase (FAH)
Function / homology
Function and homology information


fumarylacetoacetase / fumarylacetoacetase activity / homogentisate catabolic process / Tyrosine catabolism / L-tyrosine catabolic process / L-phenylalanine catabolic process / L-arginine catabolic process / lipid metabolic process / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Fumarylacetoacetase / Fumarylacetoacetase, N-terminal / Fumarylacetoacetase, N-terminal domain superfamily / Fumarylacetoacetase N-terminal / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetate (FAA) hydrolase C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Fumarylacetoacetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsScarin, R. / Rojas, A.L. / Millet, O.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)RTC2019-006826-1 Spain
H2020 Marie Curie Actions of the European Commission956758European Union
Citation
Journal: J.Med.Chem. / Year: 2026
Title: Rational Design of Small-Molecule Stabilizers of Human Fumarylacetoacetate Hydrolase for the Treatment of Tyrosinemia Type I.
Authors: Scarin, R. / Rojas, A.L. / Gil-Martinez, J. / Gomez-Galan, M. / Torres-Mozas, A. / Lopitz-Otsoa, F. / Fernandez-Ramos, D. / Jimenez-Oses, G. / Mato, J.M. / Millet, O.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Fumarylacetoacetase
F: Fumarylacetoacetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,24939
Polymers93,8132
Non-polymers2,43637
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-312 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.728, 105.020, 75.589
Angle α, β, γ (deg.)90.000, 97.110, 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, 2 molecules EF

#1: Protein Fumarylacetoacetase / FAA / Beta-diketonase / Fumarylacetoacetate hydrolase


Mass: 46906.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAH / Production host: Escherichia coli (E. coli) / References: UniProt: P16930, fumarylacetoacetase

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Non-polymers , 7 types, 526 molecules

#2: Chemical ChemComp-A1JSL / 3-[(6-methylnaphthalen-2-yl)sulfonylamino]propanoic acid


Mass: 293.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 and 7.0 at 25% to PEG 3350. / PH range: pH 5.5 and 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.3→75.01 Å / Num. obs: 45825 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.9 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.9
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4469 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→75.01 Å / SU ML: 0.2612 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 24.9992
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 2207 4.82 %
Rwork0.1988 43565 -
obs0.2008 45772 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→75.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 121 489 7154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00546878
X-RAY DIFFRACTIONf_angle_d0.71669345
X-RAY DIFFRACTIONf_chiral_restr0.048989
X-RAY DIFFRACTIONf_plane_restr0.0061225
X-RAY DIFFRACTIONf_dihedral_angle_d14.24792586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.32261130.24832718X-RAY DIFFRACTION99.26
2.35-2.40.35071370.25262690X-RAY DIFFRACTION99.79
2.4-2.460.28631320.23842713X-RAY DIFFRACTION99.51
2.46-2.530.27891530.22672713X-RAY DIFFRACTION99.51
2.53-2.610.27161450.22892687X-RAY DIFFRACTION99.54
2.61-2.690.29271310.21172730X-RAY DIFFRACTION99.51
2.69-2.790.24271270.21752724X-RAY DIFFRACTION99.55
2.79-2.90.25481210.20982728X-RAY DIFFRACTION99.55
2.9-3.030.26331320.20682732X-RAY DIFFRACTION99.55
3.03-3.190.22981690.19752708X-RAY DIFFRACTION99.93
3.19-3.390.23191420.18662708X-RAY DIFFRACTION99.75
3.39-3.650.22891370.18792725X-RAY DIFFRACTION99.86
3.65-4.020.21300.17452744X-RAY DIFFRACTION99.69
4.02-4.60.20981490.16592718X-RAY DIFFRACTION99.83
4.6-5.790.21611560.18262731X-RAY DIFFRACTION99.62
5.8-75.010.20411330.20232796X-RAY DIFFRACTION99.19

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