SAXSdb — 2io1

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sentrin-specific protease 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 364–589	Fragment：catalytic domain Mutation：C548S	Small ubiquitin-related modifier 3 precursor × 1 （P55854）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.230
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 364–589	Fragment：catalytic domain Mutation：C548S	Small ubiquitin-related modifier 3 precursor × 1 （P55854）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.230
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 364–589	Fragment：catalytic domain Mutation：C548S	Small ubiquitin-related modifier 3 precursor × 1 （P55854）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2IO1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TGZ Structure of human Senp2 in complex with SUMO-1 Deposited 2004-05-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–589（226 aa） Fragment：catalytic domain	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.276
1TGZ Structure of human Senp2 in complex with SUMO-1 Deposited 2004-05-31	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 364–589（226 aa） Fragment：catalytic domain	Not recorded	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.276
1TH0 Structure of human Senp2 Deposited 2004-05-31	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 364–589（226 aa） Fragment：catalytic domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；277 K；20% PEG 4000, 0.2M AMMONIUM SULFATE, 3% XYLITOL, 50MM SODIUM CITRATE, PH6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.247
1TH0 Structure of human Senp2 Deposited 2004-05-31	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 364–589（226 aa） Fragment：catalytic domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；277 K；20% PEG 4000, 0.2M AMMONIUM SULFATE, 3% XYLITOL, 50MM SODIUM CITRATE, PH6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.247
2IO0 Crystal structure of human Senp2 in complex with preSUMO-2 Deposited 2006-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–589（226 aa） Fragment：catalytic domain	Mutation：C548S	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；15% PEG 4000, 0.2M Lithium sulfate, 0.1mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.249
2IO2 Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1 Deposited 2006-10-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 364–589（226 aa） Fragment：catalytic domain	Mutation：C548S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；12% PEG 4000, 0.1M Lithium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.301
2IO3 Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2 Deposited 2006-10-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 364–589（226 aa） Fragment：catalytic domain	Mutation：C548S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；12% PEG 4000, 0.1M Lithium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.306
3ZO5 Structure of SENP2-Loop1 in complex with preSUMO-2 Deposited 2013-02-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 363–392（30 aa） Fragment：RESIDUES 363-589 Chain A 395–589（195 aa） Fragment：RESIDUES 363-589	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å R-free 0.236
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain W 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 366–589（224 aa） Fragment：CATALYTIC DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326

7 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SENP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–232； UniProt 364–589 Author chain C； PDBConstruct 7–232； UniProt 364–589 Author chain E； PDBConstruct 7–232； UniProt 364–589

Small ubiquitin-related modifier 3 precursor

Homo sapiens

UniProt P55854

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 14–103	Not recorded	Sentrin-specific protease 2 × 1 （Q9HC62）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.230
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 14–103	Not recorded	Sentrin-specific protease 2 × 1 （Q9HC62）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.230
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 14–103	Not recorded	Sentrin-specific protease 2 × 1 （Q9HC62）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2IO1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U4A Solution structure of human SUMO-3 C47S Deposited 2004-07-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–92（79 aa） Fragment：ubiquitin-like domain	Mutation：C47S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.25；298 K；Ionic strength (raw mmCIF value) 25mM phosphate buffer, 75mM Nacl；Pressure 1 NMR sample composition 0.8mM 15N-labeled protein \| 25mM phosphate buffer, 75mM Nacl 90% H2O, 10% D2O NMR sample composition 0.6mM 13C,15N-labeled protein \| 25mM phosphate buffer, 75mM Nacl 90% H2O, 10% D2O	Resolution not provided
2MP2 Solution structure of SUMO dimer in complex with SIM2-3 from RNF4 Deposited 2014-05-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 12–92（81 aa） Fragment：UNP residues 12-92 Chain B 2–90（89 aa） Fragment：UNP residues 2-90	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6K5R Complex of SUMO2 with Phosphorylated viral SIM IE2 Deposited 2019-05-30	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 15–91（77 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 162.7；Pressure 1 NMR sample composition 0.3 mM [U-15N] SUMO2, 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] SUMO2, 1.5 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6NNQ Non-covalent structure of SENP1 in complex with SUMO2 Deposited 2019-01-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 15–92（78 aa） Fragment：residues 15-92	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；20% PEG 6000, 0.1M HEPES, pH 7.5	Resolution 2.62 Å R-free 0.277
7R2E Structure of human Senp7 with SUMO2 Deposited 2022-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 16–91（76 aa）	Not recorded	AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium HEPES 7.0, 15 % w/v PEG 20,000	Resolution 1.74 Å R-free 0.230
7R2E Structure of human Senp7 with SUMO2 Deposited 2022-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 16–91（76 aa）	Not recorded	AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium HEPES 7.0, 15 % w/v PEG 20,000	Resolution 1.74 Å R-free 0.230
7ZJU Structure of human USPL1 in covalent complex with SUMO3-2Br probe Deposited 2022-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–91（90 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1 OXU 2-bromanylethanamine × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100 mM Tris pH 8.8, 19% PEG6000, 200 mM CaCl2	Resolution 2.17 Å R-free 0.238
7ZJU Structure of human USPL1 in covalent complex with SUMO3-2Br probe Deposited 2022-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–91（90 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 2 OXU 2-bromanylethanamine × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100 mM Tris pH 8.8, 19% PEG6000, 200 mM CaCl2	Resolution 2.17 Å R-free 0.238
9GNN Structure of SENP5 in complex with SUMO2 Deposited 2024-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 14–91（78 aa）	Not recorded	AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000	Resolution 2.36 Å R-free 0.283
9GNN Structure of SENP5 in complex with SUMO2 Deposited 2024-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 14–91（78 aa）	Not recorded	AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000	Resolution 2.36 Å R-free 0.283

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SUMO3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–94； UniProt 14–103 Author chain D； PDBConstruct 5–94； UniProt 14–103 Author chain F； PDBConstruct 5–94； UniProt 14–103

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2io1
Deposition date deposition_date	2006-10-09
Structure title title	Crystal structure of human Senp2 in complex with preSUMO-3
Keywords keywords	SUMO, Ubiquitin, Senp, Ulp, complex, PROTEIN BINDING, HYDROLASE; PROTEIN BINDING, HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.33 Å
Radius of gyration Rg (electron density) rg_electron	31.41 Å
Forward intensity I(0) i0	178635000.00
Molecular weight molecular_weight	107110.0 kDa
Excluded volume excluded_volume	134450 Å³
Envelope volume envelope_volume	169770 Å³
Hydration-shell volume shell_volume	44379 Å³
Envelope diameter envelope_diameter	102.3 Å
Shell Rg shell_rg	39.06 Å
Envelope Rg envelope_rg	30.99 Å
Shape Rg shape_rg	31.41 Å
Total Rg total_rg	32.04 Å
Total atoms total_atoms	7538
Residues n_residues	914
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	97.8 Å
Rg (real space) rg_real	32.14 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	1.7860e+08
I(0) uncertainty (real space) i0_real_error	2.7310e+06
Rg (reciprocal space) rg_reciprocal	32.22 Å
I(0) (reciprocal space) i0_reciprocal	178600000.0000
Solution quality estimate total_estimate	0.8390
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.9 Å
Skewness Skewness skewness	0.104
Kurtosis Kurtosis kurtosis	-0.642
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35780000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Sentrin-specific protease 2
Molecular weight formula_weight	27342.6 kDa
EC 编号 ec_number	3.4.22.-
Mutation mutation	C548S
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	7816

GSHMASDLLELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVINFYMNLLVERNKKQGYPALHVFSTFFYPKLKSGGYQAVKRWTKGVNLFEQEIILVPIHRKVHWSLVVIDLRKKCLKYLDSMGQKGHRICEILLQYLQDESKTKRNSDLNLLEWTHHSMKPHEIPQQLNGSDSGMFTCKYADYISRDKPITFTQHQMPLFRKKMVWEILHQQLL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Small ubiquitin-related modifier 3 precursor
Molecular weight formula_weight	10589.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

GSHMNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVPESSLAGHSF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	278

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2io1a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.7 — Adenain-like

Domain ID domain_id	d2io1b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d2io1c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.7 — Adenain-like

Domain ID domain_id	d2io1d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d2io1e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.7 — Adenain-like

Domain ID domain_id	d2io1f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (6 domains)

Domain ID domain_id	2io1A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily	10 — Adenoviral Proteinase; Chain A

Domain ID domain_id	2io1B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2io1C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily	10 — Adenoviral Proteinase; Chain A

Domain ID domain_id	2io1D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2io1E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily	10 — Adenoviral Proteinase; Chain A

Domain ID domain_id	2io1F00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

▶

8. Citations (1)

▶

Unit-cell length a length_a	141.980 Å
Unit-cell length b length_b	143.360 Å
Unit-cell length c length_c	134.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2040
R_free r_free	0.2300

fit	/app/data/saxs_computation/io/2io1/2io1.fit
pddf	/app/data/pr_computation/io/2io1/2io1.pr.out
profile	/app/data/saxs_computation/io/2io1/2io1.dat

Crystal structure of human Senp2 in complex with preSUMO-3

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sentrin-specific protease 2

State in the Current Structure

Other States of the Same Protein in the Database

Small ubiquitin-related modifier 3 precursor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)