8X4S

The L-tryptophan specific decarboxylase PsiD covalent bonding with tryptamine

• PDB DOI: https://doi.org/10.2210/pdb8X4S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Psilocybe cubensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-15 Released: 2024-11-20 
• Deposition Author(s): Meng, C.Y., Wen, Y., Guo, W.T., Wu, B.X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

The L-tryptophan specific decarboxylase PsiD covalent bonding with tryptamine

Meng, C.Y., Wen, Y., Guo, W.T., Wu, B.X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 6 assigned by authors.

Macromolecule Content

• Total Structure Weight: 299.21 kDa 
• Atom Count: 18,594 
• Modelled Residue Count: 2,285 
• Deposited Residue Count: 2,628 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-tryptophan decarboxylase	A [auth I], C [auth G], E [auth A], G [auth C], I [auth E], K	402	Psilocybe cubensis	Mutation(s): 0  Gene Names: psiD EC: 4.1.1.105
UniProt
Find proteins for P0DPA6 (Psilocybe cubensis) Explore P0DPA6  Go to UniProtKB:  P0DPA6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-tryptophan decarboxylase	B [auth J], D [auth H], F [auth B], H [auth D], J [auth F], L	36	Psilocybe cubensis	Mutation(s): 0  Gene Names: psiD EC: 4.1.1.105
UniProt
Find proteins for P0DPA6 (Psilocybe cubensis) Explore P0DPA6  Go to UniProtKB:  P0DPA6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LWG (Subject of Investigation/LOI)	M [auth J], N [auth H], O [auth B], P [auth D], Q [auth F], R [auth L]	(2~{R})-2-[2-(1~{H}-indol-3-yl)ethylamino]propanoic acid C13 H16 N2 O2 BGXZBALMOFWVRC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.681	α = 90
b = 122.502	β = 99.77
c = 128.716	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Meng, C.Y., Wen, Y., Guo, W.T., Wu, B.X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release