9Q9O: TRIM21 PRYSPRY

TRIM21 PRYSPRY bound to compound 36. Determined by X-ray diffraction at 2.46 Å resolution. Released 8 Oct 2025.

Method: X-ray diffraction
Resolution: 2.46 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,064
Mol. weight: 92.16 kDa
Ligands: A1I4Z
Released: 8 Oct 2025

Explore 9Q9O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q9O contains 14 α-helices and 63 β-strands across 4 chains. 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
α-helix	0-2	3
β-strand	3	1	4
β-strand	8	1	5
β-strand	17-19	3	4
β-strand	25-28	4	4
β-strand	48-49	2	6
β-strand	50	1	5
β-strand	54	1	6
β-strand	58-64	7	4
β-strand	71-77	7	6
α-helix	90-92	3
β-strand	94-99	6	6
β-strand	105-107	3	6
β-strand	123-129	7	4
β-strand	134-139	6	4
β-strand	145-150	6	4
β-strand	159-164	6	6
α-helix	176	1
β-strand	177-179	3	4

Chain B: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	0-2	3
β-strand	3	1	1
β-strand	8	1	2
β-strand	17-19	3	1
α-helix	20	1
β-strand	25-28	4	1
β-strand	48-49	2	3
β-strand	50	1	2
β-strand	54	1	3
β-strand	58-64	7	1
β-strand	71-77	7	3
α-helix	90-92	3
β-strand	94-100	7	3
β-strand	104-107	4	3
β-strand	123-129	7	1
β-strand	134-139	6	1
β-strand	145-150	6	1
β-strand	159-164	6	3
α-helix	176	1
β-strand	177-179	3	1

Chain C: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	0-2	3
β-strand	3	1	7
β-strand	8	1	8
β-strand	17-19	3	7
β-strand	25-28	4	7
β-strand	48-49	2	9
β-strand	50	1	8
β-strand	54	1	9
β-strand	58-64	7	7
β-strand	71-77	7	9
α-helix	90-92	3
β-strand	94-99	6	9
β-strand	105-107	3	9
β-strand	123-129	7	7
β-strand	134-139	6	7
β-strand	145-149	5	7
β-strand	159-164	6	9
α-helix	176	1
β-strand	177-179	3	7

Chain D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	0-2	3
β-strand	3	1	10
β-strand	8-9	2	11
β-strand	17-19	3	10
β-strand	25-28	4	10
β-strand	48-50	3	11
β-strand	54	1	11
β-strand	58-64	7	10
β-strand	71-77	7	11
α-helix	90-92	3
β-strand	94-100	7	11
β-strand	104-107	4	11
β-strand	123-129	7	10
β-strand	134-139	6	10
α-helix	140-142	3
β-strand	145-150	6	10
β-strand	159-164	6	11
α-helix	176	1
β-strand	177-179	3	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM21	A, B, C, D	protein	198	Homo sapiens	P19474 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9Q9O_1 E3 ubiquitin-protein ligase TRIM21 (chains A, B, C, D)
MAHHHHHHMVHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHF
HSGKHYWEVDVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTP
LHLQVPPCQVGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNT
APLTLCPLNIGSQGSTDY

Ligands and cofactors

ID	Name	Formula	Copies
A1I4Z	4-[[[4-imidazol-1-yl-3-[1-[(4-methoxyphenyl)methyl]-3-methyl-pyrazol-4-yl]pheny…	C31 H32 N6 O2	4

Primary citation

State-selective small molecule degraders that preferentially remove aggregates and oligomers. Luptak, J., Clift, D., Mukadam, A. et al. Nat Commun (2025) 16:10486-10486. DOI 10.1038/s41467-025-65454-z · 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

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