2CKG: Sentrin-specific protease 1

The structure of SENP1 SUMO-2 co-complex suggests a structural basis for discrimination between SUMO paralogues during processing. Determined by X-ray diffraction at 2.45 Å resolution. Released 26 Apr 2006.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,840
Mol. weight: 53.61 kDa
Released: 26 Apr 2006

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

Secondary structure: helices and β-sheets

2CKG contains 34 α-helices and 18 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: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	427-435	9
β-strand	443-447	5	1
β-strand	450-453	4	1
α-helix	454-457	4
α-helix	458-460	3
α-helix	464-466	3
α-helix	468-481	14
α-helix	488-489	2
β-strand	490-492	3	2
α-helix	493-494	2
α-helix	496-504	9
α-helix	506-509	4
α-helix	510-513	4
α-helix	518-520	3
β-strand	523-530	8	2
β-strand	533-540	8	2
β-strand	545-549	5	2
α-helix	557-575	19
β-strand	585-588	4	2
β-strand	598	1	3
α-helix	599-601	3
α-helix	602-614	13
α-helix	623-625	3
α-helix	626-639	14

Chain B: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	420-424	5
α-helix	425-432	8
β-strand	443-447	5	4
β-strand	450-453	4	4
α-helix	454-457	4
α-helix	458-460	3
α-helix	464-467	4
α-helix	468-481	14
β-strand	482	1	5
β-strand	484	1	5
α-helix	488-489	2
β-strand	490-492	3	6
α-helix	496-504	9
α-helix	506-508	3
α-helix	510-513	4
α-helix	518-520	3
β-strand	523-530	8	6
β-strand	533-540	8	6
β-strand	545-549	5	6
β-strand	555	1	3
α-helix	557-570	14
α-helix	571-575	5
β-strand	585-588	4	6
α-helix	589-590	2
α-helix	599-601	3
α-helix	602-615	14
α-helix	623-625	3
α-helix	626-639	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 1	A, B	protein	225	HOMO SAPIENS	Q9P0U3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2CKG_1 SENTRIN-SPECIFIC PROTEASE 1 (chains A, B)
EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNML
MERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAV
VDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQIPQQMN
GSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

Primary citation

The Structure of Senp1-Sumo-2 Complex Suggests a Structural Basis for Discrimination between Sumo Paralogues During Processing. Shen, L.N., Dong, C., Liu, H. et al. Biochem J (2006) 397:279. DOI 10.1042/BJ20052030 · 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
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
2IYD 3.2 Å, SENP1 covalent complex with SUMO-2

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