9M3N: Human TRIM21 PRYSPRY

Crystal structure of human TRIM21 PRYSPRY in complex with T-02. Determined by X-ray diffraction at 2.08 Å resolution. Released 16 Jul 2025.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,516
Mol. weight: 20.82 kDa
Ligands: A1EMT
Released: 16 Jul 2025

Explore 9M3N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M3N contains 2 α-helices and 17 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	286	1	1
β-strand	291	1	2
β-strand	300-302	3	1
β-strand	308-311	4	1
β-strand	331-332	2	3
β-strand	333	1	2
β-strand	337	1	3
β-strand	341-347	7	1
β-strand	354-360	7	3
α-helix	373-375	3
β-strand	377-383	7	3
β-strand	387-390	4	3
β-strand	396-398	3	3
β-strand	406-412	7	1
β-strand	417-422	6	1
β-strand	428-433	6	1
β-strand	442-447	6	3
α-helix	458-459	2
β-strand	460-462	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM21	A	protein	180	Homo sapiens	P19474 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9M3N_1 E3 ubiquitin-protein ligase TRIM21 (chains A)
CAVHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGKHYW
EVDVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQVPP
CQVGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLTLCP

Ligands and cofactors

ID	Name	Formula	Copies
A1EMT	1-ethyl-~{N}-methyl-5-phenyl-~{N}-[3-[3-(trifluoromethyl)phenyl]cyclobutyl]pyra…	C24 H24 F3 N3 O	1

Primary citation

TRIM21-Driven Degradation of BRD4: Development of Heterobifunctional Degraders and Investigation of Recruitment and Selectivity Mechanisms. Zhang, L., Wang, Q., Li, X. et al. J Chem Inf Model (2025) 65:7584-7604. DOI 10.1021/acs.jcim.5c00473 · PubMed

Other PDB entries of the same protein (UniProt P19474 (AlphaFold model), which also has an AlphaFold model), best resolution first:

32QO 1.3 Å, Human TRIM21 PRYSPRY domain in complex with compound 28 (Z38)
9PLM 1.32 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-021)
32QL 1.4 Å, Human TRIM21 PRYSPRY domain in complex with HGC652
9QBA 1.45 Å, Human TRIM21 PRYSPRY domain in complex with AL236
9II5 1.49 Å, Crystal structure of human TRIM21 PRYSPRY in complex with compound 1
32QM 1.5 Å, Human TRIM21 PRYSPRY domain in complex with compound 5 (Z31)
8Y58 1.6 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with acepromazine.
9PLL 1.6 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-056)
8Y5B 1.74 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (R)-hydroxyl-acepromazine.
32QN 1.8 Å, Human TRIM21 PRYSPRY domain in complex with compound 29 (Z37)
8Y59 1.89 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (S)-hydroxyl-acepromazine.
5OLM 1.95 Å, TRIM21

Browse structure collections

About this viewer

MolViewer shows 9M3N directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.