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- PDB-3hfb: Crystal structure of human tryoptophan hydroxylase type 1 with LP... -

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Basic information

Entry
Database: PDB / ID: 3hfb
TitleCrystal structure of human tryoptophan hydroxylase type 1 with LP-534193
ComponentsTryptophan 5-hydroxylase 1
KeywordsOXIDOREDUCTASE / Tryptophan Hydroxylase type 1 / Iron / Metal-binding / Monooxygenase / Phosphoprotein / Serotonin biosynthesis
Function / homology
Function and homology information


regulation of hemostasis / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / Serotonin and melatonin biosynthesis / aromatic amino acid metabolic process / serotonin biosynthetic process / platelet degranulation / bone remodeling / NGF-stimulated transcription / negative regulation of ossification ...regulation of hemostasis / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / Serotonin and melatonin biosynthesis / aromatic amino acid metabolic process / serotonin biosynthetic process / platelet degranulation / bone remodeling / NGF-stimulated transcription / negative regulation of ossification / response to immobilization stress / positive regulation of fat cell differentiation / mammary gland alveolus development / circadian rhythm / neuron projection / iron ion binding / cytosol
Similarity search - Function
Tryptophan 5-monooxygenase / Tryptophan 5-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / 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 ...Tryptophan 5-monooxygenase / Tryptophan 5-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Chem-ML4 / Tryptophan 5-hydroxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsTari, L.W. / Swanson, R.V. / Hunter, M.J.
CitationJournal: Curr Chem Genomics / Year: 2010
Title: Mechanism of Inhibition of Novel Tryptophan Hydroxylase Inhibitors Revealed by Co-crystal Structures and Kinetic Analysis.
Authors: Cianchetta, G. / Stouch, T. / Yu, W. / Shi, Z.C. / Tari, L.W. / Swanson, R.V. / Hunter, M.J. / Hoffman, I.D. / Liu, Q.
History
DepositionMay 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_source.pdbx_wavelength_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan 5-hydroxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7823
Polymers33,2881
Non-polymers4942
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.354, 58.143, 56.625
Angle α, β, γ (deg.)90.00, 96.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tryptophan 5-hydroxylase 1 / Tryptophan 5-monooxygenase 1


Mass: 33287.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17752, tryptophan 5-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-ML4 / 4-(5-{[(2'-methylbiphenyl-2-yl)methyl]amino}pyrazin-2-yl)-L-phenylalanine / (S)-2-Amino-3-(4-{5-[(2'-methyl-biphenyl-2-ylmethyl)-amino]-pyrazin-2-yl}-phenyl)-propionic acid


Mass: 438.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H26N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293.15 K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→32.02 Å / Num. obs: 21271

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / Highest resolution: 1.92 Å / SU B: 5.141 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28857 1160 5.2 %RANDOM
Rwork0.21424 ---
obs0.21803 21271 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.42 Å2
2---0.65 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Highest resolution: 1.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 34 294 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222303
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9773112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9745272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69823.394109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95715380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9931514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021779
X-RAY DIFFRACTIONr_nbd_refined0.1940.21053
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.24
X-RAY DIFFRACTIONr_mcbond_it0.6071.51391
X-RAY DIFFRACTIONr_mcangle_it1.08422208
X-RAY DIFFRACTIONr_scbond_it1.60231017
X-RAY DIFFRACTIONr_scangle_it2.4964.5904
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 87 -
Rwork0.306 1325 -
obs--80.96 %

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