2IY0: SENP1 (mutant) SUMO1 RanGAP

SENP1 (mutant) SUMO1 RanGAP. Determined by X-ray diffraction at 2.77 Å resolution. Released 7 Aug 2006.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 3,715
Mol. weight: 53.57 kDa
Released: 7 Aug 2006

Explore 2IY0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IY0 contains 27 α-helices and 14 β-strands across 3 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: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	425-435	11
β-strand	443-447	5	1
β-strand	450-453	4	1
α-helix	454-458	5
α-helix	464-465	2
β-strand	466-467	2	2
α-helix	468-481	14
α-helix	488-489	2
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	523-530	8	3
β-strand	533-540	8	3
β-strand	545-549	5	3
α-helix	559-575	17
α-helix	578-580	3
β-strand	585-588	4	3
α-helix	595-597	3
α-helix	603-615	13
α-helix	624-626	3
α-helix	627-640	14

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	23-28	6	4
β-strand	35-37	3	4
α-helix	45-55	11
α-helix	59-61	3
β-strand	62-66	5	4
β-strand	69-70	2	4
β-strand	87-92	6	4
β-strand	95-96	2	2

Chain C: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	435-439	5
α-helix	443-448	6
α-helix	453-460	8
α-helix	466-477	12
α-helix	484-502	19
α-helix	509-519	11
α-helix	536-545	10
α-helix	555-564	10
α-helix	568-571	4
α-helix	574-586	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 1	A	protein	226	HOMO SAPIENS	Q9P0U3 (AlphaFold model)
Small ubiquitin-related modifier 1	B	protein	82	HOMO SAPIENS	P63165 (AlphaFold model)
Ran gtpase-activating protein 1	C	protein	156	HOMO SAPIENS	P46060 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2IY0_1 SENTRIN-SPECIFIC PROTEASE 1 (chains A)
EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNML
MERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAV
VDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQM
NGSDAGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

Sequence of entity 2 (B), FASTA

>2IY0_2 SMALL UBIQUITIN-RELATED MODIFIER 1 (chains B)
EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKE
LGMEEEDVIEVYQEQTGGHSTV

Sequence of entity 3 (C), FASTA

>2IY0_3 RAN GTPASE-ACTIVATING PROTEIN 1 (chains C)
ADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKVSSVFKDEATVRMAVQ
DAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLYGPLMALNHMVQQDYF
PKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV

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
2IY1 2.46 Å, SENP1 (mutant) full length SUMO1
6NNQ 2.62 Å, Non-covalent structure of SENP1 in complex with SUMO2
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

Browse structure collections

About this viewer

MolViewer shows 2IY0 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.