9QBA: Human TRIM21 PRYSPRY domain

Human TRIM21 PRYSPRY domain in complex with AL236. Determined by X-ray diffraction at 1.45 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,584
Mol. weight: 20.89 kDa
Ligands: A1I41
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

9QBA contains 3 α-helices and 16 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: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	291	1	1
α-helix	293-295	3
β-strand	300-302	3	2
β-strand	308-311	4	2
β-strand	331-332	2	3
β-strand	333	1	1
β-strand	337	1	3
β-strand	341-347	7	2
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	2
β-strand	417-422	6	2
β-strand	428-433	6	2
β-strand	442-447	6	3
α-helix	458-459	2
β-strand	460-462	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM21	A	protein	179	Homo sapiens	P19474 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9QBA_1 E3 ubiquitin-protein ligase TRIM21 (chains A)
VHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGKHYWEV
DVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQVPPCQ
VGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLTLCPL

Ligands and cofactors

ID	Name	Formula	Copies
A1I41	~{N}-(cyclohexylmethyl)-4-(4-fluoranyl-2-methylsulfanyl-phenyl)-2-methylsulfony…	C22 H26 F N O3 S2	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Crystallographic fragment screening reveals ligand hotspots in TRIM21 PRY-SPRY domain. Kim, Y., Lucic, A., Lenz, C. et al. Commun Chem (2025) 8:185-185. DOI 10.1038/s42004-025-01574-3 · 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
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
9M3N 2.08 Å, Crystal structure of human TRIM21 PRYSPRY in complex with T-02

Browse structure collections

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