2IYD: SENP1 covalent complex with SUMO-2

SENP1 covalent complex with SUMO-2. Determined by X-ray diffraction at 3.2 Å resolution. Released 8 Aug 2006.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,524
Mol. weight: 36.26 kDa
Released: 8 Aug 2006

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

Secondary structure: helices and β-sheets

2IYD contains 14 α-helices and 14 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: 12 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
β-strand	467	1	2
α-helix	468-480	13
β-strand	490-492	3	3
α-helix	495-504	10
α-helix	506-509	4
α-helix	510-513	4
β-strand	523-530	8	3
β-strand	533-540	8	3
β-strand	545-549	5	3
α-helix	557-570	14
α-helix	571-575	5
β-strand	585-588	4	3
α-helix	589-590	2
α-helix	603-615	13
α-helix	618-620	3
α-helix	627-640	14

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	16-23	8	4
β-strand	27-34	8	4
α-helix	40-48	9
β-strand	57-61	5	4
β-strand	64-65	2	4
α-helix	73-75	3
β-strand	81-87	7	4
β-strand	90	1	2

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 2	B	protein	81	HOMO SAPIENS	P61956 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2IYD_1 SENTRIN-SPECIFIC PROTEASE 1 (chains A)
EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNML
MERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAV
VDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQM
NGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

Sequence of entity 2 (B), FASTA

>2IYD_2 SMALL UBIQUITIN-RELATED MODIFIER 2 (chains B)
NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPA
QLEMEDEDTIDVFQQQTGGVY

Primary citation

Senp1 Native Structure. Dong, C., Naismith, J.H. To be published.

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
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

Browse structure collections

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