8Y59

Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (S)-hydroxyl-acepromazine.

• PDB DOI: https://doi.org/10.2210/pdb8Y59/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-31 Released: 2024-10-09 
• Deposition Author(s): Lu, P., Cheng, Y., Xue, L., Ren, X., Huang, N., Han, T.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.234 
• R-Value Work: 0.186 
• R-Value Observed: 0.191 

Literature

Selective degradation of multimeric proteins via chemically induced proximity to TRIM21.

Lu, P., Cheng, Y., Xue, L., Ren, X., Chen, C., Li, J., Wu, Q., Sun, S., Hou, J., Jia, W., Li, C., Qi, X., Huang, N., Han, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 21.93 kDa 
• Atom Count: 1,593 
• Modelled Residue Count: 182 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM21	A	192	Homo sapiens	Mutation(s): 1  Gene Names: TRIM21, RNF81, RO52, SSA1 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P19474 (Homo sapiens) Explore P19474  Go to UniProtKB:  P19474
PHAROS:  P19474 GTEx:  ENSG00000132109

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D5Y (Subject of Investigation/LOI)	B [auth A]	(1~{S})-1-[10-[3-(dimethylamino)propyl]phenothiazin-2-yl]ethanol C19 H24 N2 O S ZIJWCRNUEBJMSQ-AWEZNQCLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.234 
• R-Value Work: 0.186 
• R-Value Observed: 0.191 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.908	α = 90
b = 100.908	β = 90
c = 49.955	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Lu, P., Cheng, Y., Xue, L., Ren, X., Huang, N., Han, T.

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Funding Organization	Location	Grant Number
Other government	China	Z201100005320010
Other government	China	Z221100007022004

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release