9PLL: TRIM21-NUP98 Molecular Glue Complex

TRIM21-NUP98 Molecular Glue Complex (MAN-056). Determined by X-ray diffraction at 1.6 Å resolution. Released 27 May 2026.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,026
Mol. weight: 40.78 kDa
Ligands: A1BLD
Released: 27 May 2026

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

Secondary structure: helices and β-sheets

9PLL contains 11 α-helices and 31 β-strands across 2 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 B: 5 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
α-helix	395	1
β-strand	396-398	3	3
β-strand	406-412	7	1
β-strand	417-422	6	1
α-helix	423-425	3
β-strand	428-433	6	1
β-strand	442-447	6	3
α-helix	458-459	2
β-strand	460-462	3	1
α-helix	463-464	2

Chain C: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	718	1	4
β-strand	724-727	4	5
α-helix	730-735	6
β-strand	744-752	9	5
β-strand	756-765	10	5
β-strand	770	1	4
α-helix	771-774	4
β-strand	775-778	4	6
β-strand	781-784	4	6
α-helix	788-790	3
α-helix	792-793	2
β-strand	796	1	7
β-strand	799	1	7
β-strand	802-806	5	5
β-strand	812	1	8
β-strand	819	1	8
α-helix	823-828	6
α-helix	831-841	11
β-strand	845-850	6	5
β-strand	855-860	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM21	B	protein	184	Homo sapiens	P19474 (AlphaFold model)
Isoform 2 of Nuclear pore complex protein Nup98-Nup96	C	protein	171	Homo sapiens	P52948 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9PLL_1 E3 ubiquitin-protein ligase TRIM21 (chains B)
SGTSAVHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGK
HYWEVDVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQ
VPPCQVGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLT
LCPL

Sequence of entity 2 (C), FASTA

>9PLL_2 Isoform 2 of Nuclear pore complex protein Nup98-Nup96 (chains C)
MKSSHHHHHHENLYFQSNAMHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGR
KGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPT
DKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF

Ligands and cofactors

ID	Name	Formula	Copies
A1BLD	(3P)-3-(4-chloro-2-ethoxyphenyl)-6-fluoro-2-[(piperazin-1-yl)methyl]quinazolin-…	C21 H22 Cl F N4 O2	1

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

Primary citation

TRIM21-NUP98 Molecular Glue Complex (MAN-056). Hinshaw, S.M., Martinez, M., Fernandez, D. et al. To be published.

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.
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

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