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- PDB-9sqs: Human fumarylacetoacetate hydrolase (FAH) in complex with S2.2 -

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Basic information

Entry
Database: PDB / ID: 9sqs
TitleHuman fumarylacetoacetate hydrolase (FAH) in complex with S2.2
ComponentsFumarylacetoacetase
KeywordsHYDROLASE / fumarylacetoacetate / S2.2
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: 2.1 Å
AuthorsSacarin, R. / Rojas, L.A. / 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
DepositionSep 23, 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)95,64525
Polymers93,8132
Non-polymers1,83123
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-182 kcal/mol
Surface area31110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.770, 104.500, 75.109
Angle α, β, γ (deg.)90.000, 97.020, 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: 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, 418 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1AG4 / 4-(3,4-dichlorobenzene-1-sulfonamido)-2-fluorobenzoic acid


Mass: 364.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8Cl2FNO4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging 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: Sep 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.1→74.646 Å / Num. obs: 153130 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.147 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.1-2.13729850.71311
2.137-2.17629510.74571
2.176-2.21829920.79511
2.218-2.26329500.8291
2.263-2.31329660.85611
2.313-2.366297690.89291
2.366-2.42629920.91381
2.426-2.49129540.93181
2.491-2.56429730.93981

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→66.27 Å / SU ML: 0.2927 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1349
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 2718 5 %
Rwork0.215 51630 -
obs0.2165 54348 91.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→66.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 93 395 7032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216806
X-RAY DIFFRACTIONf_angle_d0.4989240
X-RAY DIFFRACTIONf_chiral_restr0.0427976
X-RAY DIFFRACTIONf_plane_restr0.0041216
X-RAY DIFFRACTIONf_dihedral_angle_d5.2531942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.35521400.30982691X-RAY DIFFRACTION90.25
2.14-2.180.35291450.30442643X-RAY DIFFRACTION89.5
2.18-2.220.34191340.29552668X-RAY DIFFRACTION89.44
2.22-2.270.30981350.28012615X-RAY DIFFRACTION88.37
2.27-2.330.31921510.28152588X-RAY DIFFRACTION88.33
2.33-2.380.32051420.28252651X-RAY DIFFRACTION87.75
2.38-2.450.32281320.26152603X-RAY DIFFRACTION88
2.45-2.520.2981370.272601X-RAY DIFFRACTION87.17
2.52-2.60.30121290.26352610X-RAY DIFFRACTION87.56
2.6-2.690.31071590.24232593X-RAY DIFFRACTION87.48
2.69-2.80.25321320.23152621X-RAY DIFFRACTION88.21
2.8-2.930.24831260.22862688X-RAY DIFFRACTION89.5
2.93-3.080.27421500.2312669X-RAY DIFFRACTION90.32
3.08-3.280.26031450.21712802X-RAY DIFFRACTION93.41
3.28-3.530.2211540.19992849X-RAY DIFFRACTION95.03
3.53-3.890.20711520.17952910X-RAY DIFFRACTION97.55
3.89-4.450.1971540.16412927X-RAY DIFFRACTION97.38
4.45-5.60.1811490.17522923X-RAY DIFFRACTION97.03
5.6-66.270.2071520.19832978X-RAY DIFFRACTION97.45

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