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- PDB-9t1o: Crystal structure of phenylalanine hydroxylase (PAH) with Belinostat -

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Basic information

Entry
Database: PDB / ID: 9t1o
TitleCrystal structure of phenylalanine hydroxylase (PAH) with Belinostat
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Phenylketonuria / phenylalanine 4-monooxygenase / Phenylalanine metabolism / phenylalanine 4-monooxygenase activity / L-tyrosine biosynthetic process / catecholamine biosynthetic process / L-phenylalanine catabolic process / amino acid biosynthetic process / iron ion binding / cytosol
Similarity search - Function
Phenylalanine-4-hydroxylase, tetrameric form / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Tyrosine 3-monooxygenase-like / ACT domain / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily ...Phenylalanine-4-hydroxylase, tetrameric form / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Tyrosine 3-monooxygenase-like / ACT domain / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily / Biopterin-dependent aromatic amino acid hydroxylase / Biopterin-dependent aromatic amino acid hydroxylase family profile. / ACT domain profile. / ACT domain / ACT-like domain
Similarity search - Domain/homology
Belinostat / : / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsConde-Gimenez, M. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
CitationJournal: Biomed Pharmacother / Year: 2026
Title: Variant-dependent pharmacological rescue of phenylalanine hydroxylase supports a precision therapeutic strategy for phenylketonuria.
Authors: Conde-Gimenez, M. / Salillas, S. / Galiana-Cameo, M. / Martinez-Olivan, J.E. / Mahia, A. / Ledesma, M. / Galano-Frutos, J.J. / Maity, R. / Velazquez-Campoy, A. / Diaz-de-Villegas, M.D. / ...Authors: Conde-Gimenez, M. / Salillas, S. / Galiana-Cameo, M. / Martinez-Olivan, J.E. / Mahia, A. / Ledesma, M. / Galano-Frutos, J.J. / Maity, R. / Velazquez-Campoy, A. / Diaz-de-Villegas, M.D. / Hurtado-Guerrero, R. / Sancho, J.
History
DepositionOct 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,74812
Polymers35,8161
Non-polymers93311
Water3,423190
1
A: Phenylalanine-4-hydroxylase
hetero molecules

A: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,49724
Polymers71,6312
Non-polymers1,86622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)65.653, 108.103, 123.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Phenylalanine-4-hydroxylase / PAH / Phe-4-monooxygenase


Mass: 35815.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAH / Production host: Escherichia coli (E. coli) / References: UniProt: P00439, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-5OG / Belinostat


Mass: 318.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N2O4S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PIPES PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.94→61.99 Å / Num. obs: 33069 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.9
Reflection shellResolution: 1.94→2.04 Å / Rmerge(I) obs: 1.155 / Num. unique obs: 4788 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→56.18 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.156 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20318 1192 3.6 %RANDOM
Rwork0.1656 ---
obs0.16695 31846 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.036 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--1.76 Å20 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 1.94→56.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 59 190 2781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172410
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.6633594
X-RAY DIFFRACTIONr_angle_other_deg1.5451.575589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.97721.656151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33115426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3751517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02615
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_it2.5392.9851237
X-RAY DIFFRACTIONr_mcbond_other2.542.9821236
X-RAY DIFFRACTIONr_mcangle_it3.5364.4591545
X-RAY DIFFRACTIONr_mcangle_other3.5354.4621546
X-RAY DIFFRACTIONr_scbond_it3.9023.5461431
X-RAY DIFFRACTIONr_scbond_other3.9013.5481432
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8355.1132049
X-RAY DIFFRACTIONr_long_range_B_refined7.49335.6883090
X-RAY DIFFRACTIONr_long_range_B_other7.48335.53062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 87 -
Rwork0.263 2323 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: -0.3169 Å / Origin y: 25.3082 Å / Origin z: 9.4504 Å
111213212223313233
T0.052 Å20.0104 Å2-0.0012 Å2-0.0454 Å2-0.0018 Å2--0.0235 Å2
L1.0651 °2-0.0625 °2-0.1666 °2-0.2397 °20.1138 °2--0.1392 °2
S-0.036 Å °-0.1601 Å °-0.0304 Å °-0.0605 Å °0.0223 Å °-0.0361 Å °-0.039 Å °-0.0031 Å °0.0137 Å °

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