2IY1: SENP1 (mutant) full length SUMO1

SENP1 (mutant) full length SUMO1. Determined by X-ray diffraction at 2.46 Å resolution. Released 15 Aug 2006.

Method: X-ray diffraction
Resolution: 2.46 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 5,239
Mol. weight: 73.06 kDa
Released: 15 Aug 2006

Explore 2IY1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IY1 contains 34 α-helices and 28 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: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	425-434	10
β-strand	443-447	5	1
β-strand	450-453	4	1
α-helix	454-458	5
α-helix	464-466	3
β-strand	467	1	2
α-helix	468-481	14
β-strand	490-492	3	3
α-helix	497-503	7
α-helix	506-508	3
α-helix	510-513	4
α-helix	518-520	3
β-strand	523-529	7	3
β-strand	534-540	7	3
β-strand	545-549	5	3
α-helix	557-575	19
β-strand	585-588	4	3
α-helix	595-597	3
α-helix	603-615	13
α-helix	624-626	3
α-helix	627-639	13

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	17-22	6	4
β-strand	28-33	6	4
α-helix	40-50	11
α-helix	54-56	3
β-strand	57-61	5	4
β-strand	64-65	2	4
α-helix	72-75	4
β-strand	81-87	7	4
β-strand	90	1	2

Chain C: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	425-434	10
β-strand	443-447	5	5
β-strand	450-453	4	5
α-helix	454-457	4
α-helix	458-460	3
α-helix	464-466	3
β-strand	467	1	6
α-helix	468-481	14
β-strand	490-492	3	7
α-helix	497-503	7
α-helix	506-508	3
α-helix	510-513	4
α-helix	518-520	3
β-strand	523-529	7	7
β-strand	534-540	7	7
β-strand	545-549	5	7
α-helix	557-575	19
β-strand	585-588	4	7
α-helix	595-597	3
α-helix	603-615	13
α-helix	624-626	3
α-helix	627-639	13

Chain D: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	8
β-strand	28-33	6	8
α-helix	40-50	11
α-helix	54-56	3
β-strand	57-61	5	8
β-strand	64-65	2	8
α-helix	72-75	4
β-strand	82-87	6	8
β-strand	90	1	6
α-helix	94-96	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 1	A, C	protein	226	HOMO SAPIENS	Q9P0U3 (AlphaFold model)
Small ubiquitin-related modifier 1	B, D	protein	83	HOMO SAPIENS	P63165 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2IY1_1 SENTRIN-SPECIFIC PROTEASE 1 (chains A, C)
EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNML
MERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAV
VDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQM
NGSDAGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

Sequence of entity 2 (B, D), FASTA

>2IY1_2 SMALL UBIQUITIN-RELATED MODIFIER 1 (chains B, D)
EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKE
LGMEEEDVIEVYQEQTGGHSTVC

Primary citation

Sumo Protease Senp1 Induces Isomerization of the Scissile Peptide Bond. Shen, L., Tatham, M.H., Dong, C. et al. Nat Struct Mol Biol (2006) 13:1069. DOI 10.1038/NSMB1172 · PubMed

Other PDB entries of the same protein (UniProt Q9P0U3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XPH 2.4 Å, Crystal structure of human SENP1 with the bound cobalt
2CKG 2.45 Å, The structure of SENP1 SUMO-2 co-complex suggests a structural basis for discrimination…
2IYC 2.45 Å, SENP1 native structure
2XRE 2.45 Å, Detection of cobalt in previously unassigned human SENP1 structure
6NNQ 2.62 Å, Non-covalent structure of SENP1 in complex with SUMO2
2IY0 2.77 Å, SENP1 (mutant) SUMO1 RanGAP
2G4D 2.8 Å, Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1
2CKH 3.2 Å, SENP1-SUMO2 complex
2IYD 3.2 Å, SENP1 covalent complex with SUMO-2

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