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- PDB-3hf6: Crystal structure of human tryptophan hydroxylase type 1 with bou... -

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Basic information

Entry
Database: PDB / ID: 3hf6
TitleCrystal structure of human tryptophan hydroxylase type 1 with bound LP-521834 and FE
ComponentsTryptophan 5-hydroxylase 1Tryptophan hydroxylase
KeywordsOXIDOREDUCTASE / TRYPTOPHAN 5-HYDROXYLASE 1 / Alternative splicing / 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 / serotonin biosynthetic process / aromatic amino acid metabolic 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 / serotonin biosynthetic process / aromatic amino acid metabolic 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-LX0 / Tryptophan 5-hydroxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)33,7723
Polymers33,2881
Non-polymers4842
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.199, 57.893, 55.604
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-LX0 / 4-(4-amino-6-{[(1R)-1-naphthalen-2-ylethyl]amino}-1,3,5-triazin-2-yl)-L-phenylalanine


Mass: 428.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24N6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1:1 ratio of the concentrated protein solution and a reservoir comprising 24-28% (w/v) PEG 6000, and 100 mM, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 20 CK, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0000 1.5418
DetectorType: NOIR-1 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.54181
ReflectionResolution: 1.8→47.13 Å / Num. obs: 24850

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 1.8 Å
RfactorNum. reflection
Rfree0.21683 -
Rwork0.18099 -
all0.18285 24850
obs-24850
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 33 274 2574

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