8ZIC | pdb_00008zic

Structure complex of 4-hydroxytryptamine kinase PsiK complexed with Mg2+ and Tryptamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Structural basis for psilocybin biosynthesis.

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.

(2025) Nat Commun 16: 2827-2827

  • DOI: https://doi.org/10.1038/s41467-025-58239-x
  • Primary Citation Related Structures: 
    8X4Q, 8X4S, 8ZIA, 8ZIC, 8ZIE, 8ZIG, 8ZIH, 8ZII, 8ZIM, 8ZIO

  • PubMed Abstract: 

    Psilocybin shows significant therapeutic potential for psilocybin-assisted psychotherapy in addressing various psychiatric conditions. The biosynthetic approach promises rapid and efficient production of psilocybin. Understanding the enzymes that contribute to the biosynthesis of psilocybin can enhance its production process. In this study, we elucidate the crystal structures of L-tryptophan-specific decarboxylase PsiD in both its apo and tryptamine-bound states, the 4-hydroxytryptamine kinase PsiK bound to its substrate, and several forms of the methyltransferase PsiM in either apo or substrate-bound forms derived from the psychedelic mushroom. Structure-based evaluations reveal the mechanisms of self-cleavage and self-inhibition in PsiD, along with the sequential catalytic steps from 4-hydroxytryptamine to the final compound, psilocybin. Additionally, we showcase the antidepressant properties of biosynthetic intermediates of psilocybin on female mice experiencing depression-like behaviors induced by sub-chronic variable stress. Our studies establish a structural basis for the future biosynthetic production of psilocybin using these enzymes and emphasize the clinical potential of norbaeocystin.


  • Organizational Affiliation
    • Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 41.16 kDa 
  • Atom Count: 3,079 
  • Modeled Residue Count: 361 
  • Deposited Residue Count: 362 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-hydroxytryptamine kinase362Psilocybe cubensisMutation(s): 0 
Gene Names: psiK
EC: 2.7.1 (PDB Primary Data), 2.7.1.222 (PDB Primary Data)
UniProt
Find proteins for P0DPA8 (Psilocybe cubensis)
Explore P0DPA8 
Go to UniProtKB:  P0DPA8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DPA8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
TSS
(Subject of Investigation/LOI)

Query on TSS



Download:Ideal Coordinates CCD File
B [auth A]2-(1H-INDOL-3-YL)ETHANAMINE
C10 H12 N2
APJYDQYYACXCRM-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.205α = 90
b = 100.205β = 90
c = 76.385γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release