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- PDB-9t9x: Human fumarylacetoacetate hydrolase (FAH) in complex with Acetoacetate -

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Basic information

Entry
Database: PDB / ID: 9t9x
TitleHuman fumarylacetoacetate hydrolase (FAH) in complex with Acetoacetate
ComponentsFumarylacetoacetase
KeywordsHYDROLASE / Human fumarylacetoacetate hydrolase
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
ACETOACETIC ACID / DI(HYDROXYETHYL)ETHER / Fumarylacetoacetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGil, J.M. / Scarin, 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
DepositionNov 17, 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

Downloads & links

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Assembly

Deposited unit
A: Fumarylacetoacetase
B: Fumarylacetoacetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,37632
Polymers98,1762
Non-polymers2,20030
Water15,331851
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-107 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.576, 105.148, 75.560
Angle α, β, γ (deg.)90.000, 97.619, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 49088.070 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, 881 molecules

#2: Chemical ChemComp-AAE / ACETOACETIC ACID


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
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: 5.5 and 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→65.99 Å / Num. obs: 68858 / % possible obs: 92.6 % / Redundancy: 7.1 % / CC1/2: 0.997 / Net I/σ(I): 8.9
Reflection shellResolution: 1.81→1.98 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3444 / CC1/2: 0.65 / % possible all: 63.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→65.99 Å / SU ML: 0.1857 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2039 3328 4.83 %
Rwork0.1658 65513 -
obs0.1676 68841 73.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.81→65.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 123 851 7566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386911
X-RAY DIFFRACTIONf_angle_d0.71179356
X-RAY DIFFRACTIONf_chiral_restr0.047986
X-RAY DIFFRACTIONf_plane_restr0.00641223
X-RAY DIFFRACTIONf_dihedral_angle_d15.0352589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.840.283710.187620X-RAY DIFFRACTION0.56
1.84-1.870.446370.265199X-RAY DIFFRACTION2.87
1.87-1.90.4185230.2615348X-RAY DIFFRACTION9.57
1.9-1.930.3409370.2558644X-RAY DIFFRACTION17.5
1.93-1.960.2808550.23261105X-RAY DIFFRACTION29.95
1.96-20.2949750.22821511X-RAY DIFFRACTION41.37
2-2.030.2339940.2132014X-RAY DIFFRACTION54.48
2.03-2.080.2461200.20722488X-RAY DIFFRACTION67.13
2.08-2.120.27911310.20052914X-RAY DIFFRACTION78.72
2.12-2.170.26261710.19333331X-RAY DIFFRACTION90.54
2.17-2.230.24992070.19163520X-RAY DIFFRACTION95.83
2.23-2.290.25371920.18443575X-RAY DIFFRACTION97.34
2.29-2.350.21271880.17953619X-RAY DIFFRACTION98.22
2.35-2.430.20581840.17853625X-RAY DIFFRACTION98.37
2.43-2.520.22181940.17343614X-RAY DIFFRACTION98.42
2.52-2.620.21721720.17313656X-RAY DIFFRACTION98.58
2.62-2.740.21661760.16583638X-RAY DIFFRACTION98.76
2.74-2.880.21591750.15723688X-RAY DIFFRACTION98.77
2.88-3.060.20851890.15913653X-RAY DIFFRACTION98.84
3.06-3.30.17762170.15093630X-RAY DIFFRACTION99.15
3.3-3.630.17221760.1473684X-RAY DIFFRACTION99.15
3.63-4.150.16022080.12953675X-RAY DIFFRACTION99.28
4.15-5.230.15011680.12843732X-RAY DIFFRACTION99.46
5.23-65.990.20751680.19643730X-RAY DIFFRACTION98.29

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