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- PDB-9sw1: Human fumarylacetoacetate hydrolase (FAH) in complex with A4 -

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Basic information

Entry
Database: PDB / ID: 9sw1
TitleHuman fumarylacetoacetate hydrolase (FAH) in complex with A4
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
: / Fumarylacetoacetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
CitationJournal: 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.
History
DepositionOct 4, 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
A: Fumarylacetoacetase
B: Fumarylacetoacetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,01415
Polymers93,8132
Non-polymers1,20113
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.377, 104.117, 75.077
Angle α, β, γ (deg.)90.000, 96.743, 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 AB

#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 , 5 types, 294 molecules

#2: Chemical ChemComp-A1JQ6 / 4-[(4-carboxyphenyl)sulfonylamino]-2-oxidanyl-benzoic acid


Mass: 337.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11NO7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion / 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: Nov 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.99→60.62 Å / Num. obs: 45149 / % possible obs: 92.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 39.14 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.6
Reflection shellResolution: 1.99→2.22 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2257 / CC1/2: 0.507 / % possible all: 61.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→60.62 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 2245 4.97 %
Rwork0.1741 42900 -
obs0.1762 45145 64.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.9 Å2
Refinement stepCycle: LAST / Resolution: 1.99→60.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6559 0 67 281 6907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386805
X-RAY DIFFRACTIONf_angle_d0.6739245
X-RAY DIFFRACTIONf_chiral_restr0.0444977
X-RAY DIFFRACTIONf_plane_restr0.0061223
X-RAY DIFFRACTIONf_dihedral_angle_d14.96122537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.030.259930.285622X-RAY DIFFRACTION0.6
2.03-2.080.344890.266141X-RAY DIFFRACTION3.48
2.08-2.130.4479140.2768424X-RAY DIFFRACTION10.22
2.13-2.190.2881430.2842867X-RAY DIFFRACTION21.12
2.19-2.250.2596600.27111402X-RAY DIFFRACTION33.63
2.25-2.330.27181010.25232055X-RAY DIFFRACTION50.22
2.33-2.410.27361540.25062673X-RAY DIFFRACTION64.62
2.41-2.510.29421800.23593141X-RAY DIFFRACTION76.7
2.51-2.620.30041990.21933500X-RAY DIFFRACTION85.31
2.62-2.760.27841720.21283837X-RAY DIFFRACTION92.12
2.76-2.930.23132230.19784043X-RAY DIFFRACTION98.91
2.93-3.160.22132150.18764152X-RAY DIFFRACTION99.86
3.16-3.470.21822210.16674136X-RAY DIFFRACTION99.93
3.47-3.980.18282140.15154128X-RAY DIFFRACTION99.86
3.98-5.010.19212130.13064174X-RAY DIFFRACTION99.95
5.01-60.620.19512240.16914205X-RAY DIFFRACTION99.66

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