2XRE: Sentrin-specific protease 1

Detection of cobalt in previously unassigned human SENP1 structure. Determined by X-ray diffraction at 2.45 Å resolution. Released 6 Oct 2010.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,952
Mol. weight: 55.74 kDa
Ligands: CO
Released: 6 Oct 2010

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

Secondary structure: helices and β-sheets

2XRE contains 28 α-helices and 16 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: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	420-422	3
α-helix	425-435	11
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
β-strand	490-492	3	2
α-helix	499-502	4
α-helix	506-508	3
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	599	1	3
α-helix	600-602	3
α-helix	603-615	13
α-helix	624-626	3
α-helix	627-640	14

Chain B: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	420-422	3
α-helix	425-433	9
β-strand	443-447	5	4
β-strand	450-453	4	4
α-helix	454-458	5
α-helix	468-482	15
α-helix	488-489	2
β-strand	490-492	3	5
α-helix	496-504	9
α-helix	506-508	3
α-helix	510-512	3
α-helix	518-520	3
β-strand	523-530	8	5
β-strand	533-540	8	5
β-strand	545-549	5	5
β-strand	555	1	3
α-helix	557-569	13
β-strand	586-588	3	5
α-helix	600-602	3
α-helix	603-616	14
α-helix	624-626	3
α-helix	627-640	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 1	A, B	protein	230	HOMO SAPIENS	Q9P0U3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2XRE_1 SENTRIN-SPECIFIC PROTEASE 1 (chains A, B)
DSEDEFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFY
MNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHW
CLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEI
PQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

Ligands and cofactors

ID	Name	Formula	Copies
CO	Cobalt (II) ion	Co	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

The Role of Co2+ in the Crystallization of Human Senp1 and Comments on the Limitations of Automated Refinement Protocols. Rimsa, V., Eadsforth, T., Hunter, W.N. Acta Crystallogr Sect F Struct Biol Cryst Commun (2011) 67:442. DOI 10.1107/S1744309111005835 · 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
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

Browse structure collections

About this viewer

MolViewer shows 2XRE 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.