9GNX: Human SENP5

Human SENP5 in complex with SUMO1 (E67D). Determined by X-ray diffraction at 1.9 Å resolution. Released 16 Jul 2025.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,231
Mol. weight: 33.68 kDa
Released: 16 Jul 2025

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

Secondary structure: helices and β-sheets

9GNX contains 17 α-helices and 12 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 A: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	571-574	4
α-helix	575-577	3
α-helix	581-583	3
β-strand	584	1	1
α-helix	585-598	14
β-strand	603-605	3	2
α-helix	610-617	8
α-helix	619-622	4
α-helix	623-626	4
α-helix	631-633	3
β-strand	636-643	8	2
β-strand	646-653	8	2
β-strand	658-662	5	2
α-helix	670-686	17
α-helix	690-692	3
β-strand	697-700	4	2
α-helix	713-725	13
α-helix	734-736	3
α-helix	737-750	14

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	3
α-helix	32	1
β-strand	33-39	7	3
α-helix	45-55	11
α-helix	59-61	3
β-strand	62-66	5	3
β-strand	69-70	2	3
α-helix	71-72	2
β-strand	86-92	7	3
β-strand	95	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 5	A	protein	207	Homo sapiens	Q96HI0 (AlphaFold model)
Small ubiquitin-related modifier 1	B	protein	80	Homo sapiens	P63165 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GNX_1 Sentrin-specific protease 5 (chains A)
HHHHHHSSGLVPRGSHMASMLDMDDLATLDGQNWLNDQVINMYGELIMDAVPDKVHFFNS
FFHRQLVTKGYNGVKRWTKKVDLFKKSLLLIPIHLEVHWSLITVTLSNRIISFYDSQGIH
FKFCVENIRKYLLTEAREKNRPEFLQGWQTAVTKCIPQQKNDSDCGVFVLQYCKCLALEQ
PFQFSQEDMPRVRKRIYKELCECRLMD

Sequence of entity 2 (B), FASTA

>9GNX_2 Small ubiquitin-related modifier 1 (chains B)
MGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFDGQRIADNHTP
KELGMEEEDVIEVYQEQTGX

Primary citation

Structural basis for the human SENP5's SUMO isoform discrimination. Sanchez-Alba, L., Ying, L., Maletic, M.D. et al. Nat Commun (2025) 16:4764-4764. DOI 10.1038/s41467-025-60029-4 · PubMed

Other PDB entries of the same protein (UniProt Q96HI0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GNV 2.18 Å, Human SENP5 in complex with SUMO1
9GNN 2.36 Å, Structure of SENP5 in complex with SUMO2

Browse structure collections

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