SAXSdb — 2io3

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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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 364–589	Fragment：catalytic domain Mutation：C548S	Small ubiquitin-related modifier 2 × 4 （P61956） Ran GTPase-activating protein 1 × 4 （P46060）	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

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 2IO3	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 oligomeric state 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 oligomeric state 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
2IO1 Crystal structure of human Senp2 in complex with preSUMO-3 Deposited 2006-10-09	Different oligomeric state 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	No recorded non-water small molecule	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
2IO1 Crystal structure of human Senp2 in complex with preSUMO-3 Deposited 2006-10-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 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；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
2IO1 Crystal structure of human Senp2 in complex with preSUMO-3 Deposited 2006-10-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 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；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
2IO2 Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1 Deposited 2006-10-09	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
3ZO5 Structure of SENP2-Loop1 in complex with preSUMO-2 Deposited 2013-02-20	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 22 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

Small ubiquitin-related modifier 2

Homo sapiens

UniProt P61956

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain B； UniProt 15–93	Not recorded	Sentrin-specific protease 2 × 4 （Q9HC62） Ran GTPase-activating protein 1 × 4 （P46060）	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

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 2IO3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WM2 Crystal structure of human SUMO-2 protein Deposited 2004-07-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 12–89（78 aa） Fragment：no N-terminal arm(residues 12-89)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；40% PEG600, 0.1M CHES, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.60 Å R-free 0.190
1WM3 Crystal structure of human SUMO-2 protein Deposited 2004-07-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 17–88（72 aa） Fragment：no N-terminal arm(residues 17-88)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；40% PEG600, 0.1M CHES, 0.1M Na-HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.20 Å R-free 0.185
1WZ0 Solution Structure of Human SUMO-2 (SMT3B), a Ubiquitin-like Protein Deposited 2005-02-21	Different construct 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 1–91（91 aa） Fragment：ubiquitin-like molecule	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 1.21mM protein U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2AWT Solution Structure of Human Small Ubiquitin-Like Modifier Protein Isoform 2 (SUMO-2) Deposited 2005-09-02	Different construct 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 1–95（95 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate, 150mM NaCl；Pressure ambient NMR sample composition 0.8mM SUMO-2 U-15N, 13C; 50mM phosphate buffer pH 6.0; 150mM NaCl; 1mM EDTA; 1mM DSS; 0.01% sodium azide; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2CKH SENP1-SUMO2 complex Deposited 2006-04-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 15–93（79 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.00	Resolution 3.20 Å R-free 0.294
2D07 Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase Deposited 2005-07-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–93（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；1.5M sodium malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.241
2IO0 Crystal structure of human Senp2 in complex with preSUMO-2 Deposited 2006-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 15–95（81 aa）	Not recorded	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
2IYD SENP1 covalent complex with SUMO-2 Deposited 2006-07-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 15–95（81 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 15-95	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.288
2N1W Solution structure of human SUMO2 Deposited 2015-04-24	Different construct 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 1–93（93 aa） Fragment：UNP residues 1-93	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；290 K；Pressure ambient NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] SUMO2-1, 10 mM potassium phosphate-2, 100 mM potassium chloride-3, 2 mM DTT-4, 0.1 mM EDTA-5, 0.001 % sodium azide-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM [U-100% 15N] SUMO2-7, 10 mM potassium phosphate-8, 100 mM potassium chloride-9, 2 mM DTT-10, 0.1 mM EDTA-11, 0.001 % sodium azide-12, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM [U-100% 15N] SUMO2-13, 10 mM potassium phosphate-14, 100 mM potassium chloride-15, 2 mM DTT-16, 0.1 mM EDTA-17, 0.001 % sodium azide-18, 10 w/v Pf1 phage-19, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM SUMO2-20, 10 mM potassium phosphate-21, 100 mM potassium chloride-22, 2 mM DTT-23, 0.1 mM EDTA-24, 0.001 % sodium azide-25, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N9E Structure of SUMO-2 bound to phosphorylated RAP80 SIM Deposited 2015-11-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–95（95 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 25；Pressure ambient NMR sample composition 1.2 mM peptide, 0.4 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RPQ Solution Structure of a SUMO-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3 Deposited 2008-07-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–93（93 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.7 mM [U-100% 13C; U-100% 15N] SIMMCAF1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3UIN Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 Deposited 2011-11-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 14–93（80 aa） Fragment：UNP residues 14-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.60 Å R-free 0.264
3UIO Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 14–93（80 aa） Fragment：UNP residues 14-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；14% PEG4000, 100 mM sodium citrate pH 6.0, 200 mM ammonium acetate, vapor diffusion, hanging drop, temperature 279K	Resolution 2.60 Å R-free 0.251
3ZO5 Structure of SENP2-Loop1 in complex with preSUMO-2 Deposited 2013-02-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 16–95（80 aa） Fragment：RESIDUES 16-95	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å R-free 0.236
4BKG crystal structure of human diSUMO-2 Deposited 2013-04-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 12–93（82 aa） Fragment：SUMO-2DELTAN11, RESIDUES 12-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.1 M TRIS/HCL PH 8.0, 28% PEG 350MME,0.05% DIOXANE	Resolution 2.11 Å R-free 0.231
4NPN Crystal structure of human tetra-SUMO-2 Deposited 2013-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 12–93（82 aa） Fragment：DELTAN11SUMO-2, UNP RESIDUES 12-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.4；289 K；0.1M Tris-HCl, 0.1M CHES, 30% PEG 600, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.63 Å R-free 0.218
4NPN Crystal structure of human tetra-SUMO-2 Deposited 2013-11-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 12–93（82 aa） Fragment：DELTAN11SUMO-2, UNP RESIDUES 12-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.4；289 K；0.1M Tris-HCl, 0.1M CHES, 30% PEG 600, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.63 Å R-free 0.218
5D2M Complex between human SUMO2-RANGAP1, UBC9 and ZNF451 Deposited 2015-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 15–93（79 aa） Fragment：UNP residues 15-93 Chain E 15–93（79 aa） Fragment：UNP residues 15-93	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6 % (w/v) PEG 8000, 0.2 M ammonium citrate and 0.1 M HEPES pH 7.5	Resolution 2.40 Å R-free 0.234
5ELU Isoform-specific inhibition of SUMO-dependent protein-protein interactions Deposited 2015-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 14–89（76 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M sodium cacodylate pH 6.5, 0.2 M sodium chloride and 2.0 M ammonium sulphate	Resolution 2.35 Å R-free 0.207
5EQL Isoform-specific inhibition of SUMO-dependent protein-protein interactions Deposited 2015-11-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 14–89（76 aa） Fragment：UNP residues 14-89	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；0.1 M HEPES sodium salt pH 7.6, 22% w/v polyethylene glycol 3350	Resolution 2.49 Å R-free 0.243
5GHB SOLUTION STRUCTURE OF LYS42 ACETYLATED HUMAN SUMO2 Deposited 2016-06-19	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 1–93（93 aa） Fragment：UNP RESIDUES 1-93	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；290 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure AMBIENT NMR sample composition 1 mM [U-100% 13C; U-100% 15N; U-80% 2H] SUMO2 K42Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] SUMO2 K42Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] SUMO2 K42Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 10 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM K42Ac SUMO2, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5GHC SOLUTION STRUCTURE OF LYS33 ACETYLATED HUMAN SUMO2 Deposited 2016-06-19	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 1–93（93 aa） Fragment：UNP RESIDUES 1-93	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；290 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure AMBIENT NMR sample composition 1 mM SUMO2 K33Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM SUMO2 K33Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM SUMO2 K33Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 10 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM SUMO2 K33Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6JXW Complex of SUMO2 bound SLS4 from ICP0. Deposited 2019-04-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–95（95 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 137；Pressure 1 NMR sample composition 0.5 mM [U-98% 15N] SUMO2, 2.0 mM SLS4-SIM from Ubiquitin E3 ligase ICP0, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] SUMO2, 2.0 mM SLS4-SIM from Ubiquitin E3 ligase ICP0, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-15N; U-2H] SUMO2, 2.0 mM SLS4-SIM from Ubiquitin E3 ligase ICP0, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2.0 mM [U-15N; U-2H] SUMO2, 0.5 mM SLS4-SIM from Ubiquitin E3 ligase ICP0, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6JXX SUMO2 bound to phosphorylated SLS4-SIM peptide from ICP0 Deposited 2019-04-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–95（95 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 137；Pressure 1 NMR sample composition 0.5 mM [U-15N] SUMO2, 2 mM Phosphorylated SLS4 from E3 ubiquitin ligase ICP0, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM [U-13C; U-15N] SUMO2, 1.5 mM Phosphorylated SLS4 from E3 ubiquitin ligase ICP0, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7ZJV Structure of human USPL1 in covalent complex with DeltaN-SUMO2/3-PA probe Deposited 2022-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–92（75 aa）	Not recorded	ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；293 K；100 mM CHES pH 8.9, 34% PEG600	Resolution 2.40 Å R-free 0.258

24 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SUMO2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–81； UniProt 15–93

Ran GTPase-activating protein 1

Homo sapiens

UniProt P46060

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C； UniProt 418–587	Fragment：c-terminal domain Mutation：C573S	Sentrin-specific protease 2 × 4 （Q9HC62） Small ubiquitin-related modifier 2 × 4 （P61956）	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

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 2IO3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z5S Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2 Deposited 2005-03-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 418–587（170 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；18% PEG4000 (w/v), 0.1 M sodium citrate, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.01 Å R-free 0.290
2GRN Crystal Structure of human RanGAP1-Ubc9 Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 419–587（169 aa） Fragment：C-terminal domain (residues 419-587)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.218
2GRO Crystal Structure of human RanGAP1-Ubc9-N85Q Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 419–587（169 aa） Fragment：C-terminal domain (residues 419-587)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.202
2GRP Crystal Structure of human RanGAP1-Ubc9-Y87A Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 419–587（169 aa） Fragment：C-terminal domain (RESIDUES 419-587)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.05 Å R-free 0.231
2GRQ Crystal Structure of human RanGAP1-Ubc9-D127A Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 419–587（169 aa） Fragment：C-terminal domain (RESIDUES 419-587)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.205
2GRR Crystal Structure of human RanGAP1-Ubc9-D127S Deposited 2006-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 419–587（169 aa） Fragment：C-terminal domain (RESIDUES 419-587)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.30 Å R-free 0.222
2IO2 Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1 Deposited 2006-10-09	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 418–587（170 aa） Fragment：c-terminal domain	Mutation：C573S	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
2IY0 SENP1 (mutant) SUMO1 RanGAP Deposited 2006-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 432–587（156 aa） Fragment：C-TERMINUS, RESIDUES 432-587	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.77 Å R-free 0.279
3UIN Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 Deposited 2011-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 419–587（169 aa） Fragment：UNP residues 419-587	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.60 Å R-free 0.264
3UIO Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 419–587（169 aa） Fragment：UNP residues 419-587	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；14% PEG4000, 100 mM sodium citrate pH 6.0, 200 mM ammonium acetate, vapor diffusion, hanging drop, temperature 279K	Resolution 2.60 Å R-free 0.251
3UIP Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 419–587（169 aa） Fragment：UNP residues 419-587	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；22% PEG4000, 100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.29 Å R-free 0.232
5D2M Complex between human SUMO2-RANGAP1, UBC9 and ZNF451 Deposited 2015-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 418–587（170 aa） Fragment：UNP residues 418-587	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6 % (w/v) PEG 8000, 0.2 M ammonium citrate and 0.1 M HEPES pH 7.5	Resolution 2.40 Å R-free 0.234
5D2M Complex between human SUMO2-RANGAP1, UBC9 and ZNF451 Deposited 2015-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 418–587（170 aa） Fragment：UNP residues 418-587	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6 % (w/v) PEG 8000, 0.2 M ammonium citrate and 0.1 M HEPES pH 7.5	Resolution 2.40 Å R-free 0.234
9B62 Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model Deposited 2024-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–587（587 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging	Resolution 2.90 Å

13 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RGP1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–172； UniProt 418–587

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	2io3
Deposition date deposition_date	2006-10-09
Structure title title	Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2
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	26.52 Å
Radius of gyration Rg (electron density) rg_electron	25.75 Å
Forward intensity I(0) i0	43619500.00
Molecular weight molecular_weight	52073.0 kDa
Excluded volume excluded_volume	65756 Å³
Envelope volume envelope_volume	86959 Å³
Hydration-shell volume shell_volume	28501 Å³
Envelope diameter envelope_diameter	86.9 Å
Shell Rg shell_rg	32.59 Å
Envelope Rg envelope_rg	25.96 Å
Shape Rg shape_rg	25.73 Å
Total Rg total_rg	26.64 Å
Total atoms total_atoms	3664
Residues n_residues	454
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	81.5 Å
Rg (real space) rg_real	26.46 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	4.3620e+07
I(0) uncertainty (real space) i0_real_error	7.0400e+05
Rg (reciprocal space) rg_reciprocal	26.48 Å
I(0) (reciprocal space) i0_reciprocal	43620000.0000
Solution quality estimate total_estimate	0.9132
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.525
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6057000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.987

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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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3664

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 2
Molecular weight formula_weight	9265.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MANDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG

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 polymer

Description description	Ran GTPase-activating protein 1
Molecular weight formula_weight	18670.5 kDa
Mutation mutation	C573S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SLNTGEPAPVLSSPPPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKVSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLYGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESSSFARHSLLQTLYKV

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

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2io3a1
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	d2io3b1
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	d2io3c1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.12 — Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
Family Family family	a.118.12.1 — Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	2io3A00
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	2io3B00
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	2io3C00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	200 — Ran-GTPase activating protein 1, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	164.056 Å
Unit-cell length b length_b	164.056 Å
Unit-cell length c length_c	78.094 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	24.810 Å
R factor r_factor	0.2770
R_work r_work	0.2770
R_free r_free	0.3060

fit	/app/data/saxs_computation/io/2io3/2io3.fit
pddf	/app/data/pr_computation/io/2io3/2io3.pr.out
profile	/app/data/saxs_computation/io/2io3/2io3.dat

Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2

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 2

State in the Current Structure

Other States of the Same Protein in the Database

Ran GTPase-activating protein 1

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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)