2XPH: Human SENP1 with the bound cobalt

Crystal structure of human SENP1 with the bound cobalt. Determined by X-ray diffraction at 2.4 Å resolution. Released 8 Sept 2010.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,978
Mol. weight: 56.77 kDa
Ligands: CO
Released: 8 Sept 2010

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

Secondary structure: helices and β-sheets

2XPH contains 29 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	425-434	10
β-strand	445-447	3	1
β-strand	450-452	3	1
α-helix	454-458	5
α-helix	468-481	14
α-helix	488-489	2
β-strand	490-492	3	2
α-helix	499-502	4
α-helix	506-509	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	557-570	14
α-helix	571-575	5
α-helix	578-579	2
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: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	420-422	3
α-helix	425-434	10
β-strand	443-447	5	4
β-strand	450-453	4	4
α-helix	454-457	4
α-helix	458-460	3
α-helix	465-467	3
α-helix	468-481	14
β-strand	490-492	3	5
α-helix	497-504	8
α-helix	506-508	3
α-helix	510-513	4
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	557-575	19
α-helix	578-579	2
β-strand	585-588	4	5
α-helix	600-602	3
α-helix	603-614	12
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	238	HOMO SAPIENS	Q9P0U3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2XPH_1 SENTRIN-SPECIFIC PROTEASE 1 (chains A, B)
GAMADIGSDSEDEFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWL
NDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLV
PIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQL
FSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

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., Hay, R.T. et al. 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:

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
2IYD 3.2 Å, SENP1 covalent complex with SUMO-2

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