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- PDB-8zic: Structure complex of 4-hydroxytryptamine kinase PsiK complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8zic
TitleStructure complex of 4-hydroxytryptamine kinase PsiK complexed with Mg2+ and Tryptamine
Components4-hydroxytryptamine kinase
KeywordsMETAL BINDING PROTEIN / Kinase / 4-hydroxytryptamine / psilocybin
Function / homology
Function and homology information


4-hydroxytryptamine kinase / 4-hydroxytryptamine kinase activity / psilocybin biosynthetic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / ATP binding
Similarity search - Function
CHK kinase-like / ZnF_C4 abd HLH domain containing kinases domain / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 2-(1H-INDOL-3-YL)ETHANAMINE / 4-hydroxytryptamine kinase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMeng, C.Y. / Wen, Y. / Guo, W.T. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for psilocybin biosynthesis.
Authors: Meng, C. / Guo, W. / Xiao, C. / Wen, Y. / Zhu, X. / Zhang, Q. / Liang, Y. / Li, H. / Xu, S. / Qiu, Y. / Chen, H. / Lin, W.J. / Wu, B.
History
DepositionMay 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxytryptamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1636
Polymers40,4871
Non-polymers6765
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-38 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.205, 100.205, 76.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-hydroxytryptamine kinase / Psilocybin biosynthesis kinase


Mass: 40486.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Gene: psiK / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DPA8, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, 4-hydroxytryptamine kinase

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Non-polymers , 5 types, 196 molecules

#2: Chemical ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris base/Hydrochloric acid pH 8.5, 0.1 M Magnesium chloride, and 20% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.23→60.75 Å / Num. obs: 19400 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.084 / Net I/σ(I): 18.2
Reflection shellResolution: 2.23→2.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2576 / CC1/2: 0.82 / Rpim(I) all: 0.253 / Rrim(I) all: 0.493 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RoseTTAFold

Resolution: 2.23→60.75 Å / SU ML: 0.2478 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 975 5.04 %
Rwork0.1696 18379 -
obs0.1717 19354 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.48 Å2
Refinement stepCycle: LAST / Resolution: 2.23→60.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 42 191 3073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732945
X-RAY DIFFRACTIONf_angle_d0.90363996
X-RAY DIFFRACTIONf_chiral_restr0.0517447
X-RAY DIFFRACTIONf_plane_restr0.0058508
X-RAY DIFFRACTIONf_dihedral_angle_d17.13221089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.350.3021190.22232403X-RAY DIFFRACTION92.28
2.35-2.490.23831440.19592587X-RAY DIFFRACTION99.6
2.49-2.680.24631440.19012618X-RAY DIFFRACTION100
2.68-2.950.2781550.1942609X-RAY DIFFRACTION99.93
2.95-3.380.25151420.18412636X-RAY DIFFRACTION100
3.38-4.260.17291290.14182693X-RAY DIFFRACTION100
4.26-60.750.16761420.15332833X-RAY DIFFRACTION99.7

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