SAXSdb — 2iyd

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

SENTRIN-SPECIFIC PROTEASE 1

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 419–592 Chain A； UniProt 593–643	Fragment：CATALYTIC FRAGMENT, RESIDUES 419-643	SMALL UBIQUITIN-RELATED MODIFIER 2 × 1 （P61956）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.20 Å R-free 0.288

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 2IYD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CKG The structure of SENP1 SUMO-2 co-complex suggests a structural basis for discrimination between SUMO paralogues during processing Deposited 2006-04-18	Different construct 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 419–643（225 aa） Fragment：RESIDUES 419-643	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.50	Resolution 2.45 Å R-free 0.279
2CKG The structure of SENP1 SUMO-2 co-complex suggests a structural basis for discrimination between SUMO paralogues during processing Deposited 2006-04-18	Different construct 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 419–643（225 aa） Fragment：RESIDUES 419-643	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.50	Resolution 2.45 Å R-free 0.279
2CKH SENP1-SUMO2 complex Deposited 2006-04-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 419–643（225 aa） Fragment：PROTEASE DOMAIN, RESIDUES 419-643	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
2G4D Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1 Deposited 2006-02-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 440–643（204 aa） Fragment：protease catalytic domain	Mutation：C603S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；289 K；0.1M CAPS, 40% PEG400, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.278
2G4D Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1 Deposited 2006-02-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 440–643（204 aa） Fragment：protease catalytic domain	Mutation：C603S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；289 K；0.1M CAPS, 40% PEG400, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.278
2IY0 SENP1 (mutant) SUMO1 RanGAP Deposited 2006-07-11	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 419–592（174 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 419-643 Chain A 593–643（51 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 419-643	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.77 Å R-free 0.279
2IY1 SENP1 (mutant) full length SUMO1 Deposited 2006-07-11	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 419–592（174 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 419-643 Chain A 593–643（51 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 419-643	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.46 Å R-free 0.281
2IY1 SENP1 (mutant) full length SUMO1 Deposited 2006-07-11	Different construct Different mutation/modification Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 419–592（174 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 419-643 Chain C 593–643（51 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 419-643	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.46 Å R-free 0.281
2IYC SENP1 native structure Deposited 2006-07-14	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 419–592（174 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 419-643 Chain A 593–643（51 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 419-643 Chain B 419–592（174 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 419-643 Chain B 593–643（51 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 419-643	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å R-free 0.267
2XPH Crystal structure of human SENP1 with the bound cobalt Deposited 2010-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 415–644（230 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	Not recorded	GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions CRYSTALS FORMED FROM 1 TO 1 OF RESERVOIR SOLUTION (1.8 M AMMONIUM SULFATE, 50 MM COCL2 AND 100 MM MES PH 6.5) AND PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL (PH 8.0), AND 50 MM NACL).	Resolution 2.40 Å R-free 0.313
2XPH Crystal structure of human SENP1 with the bound cobalt Deposited 2010-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 415–644（230 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	Not recorded	GOL GLYCEROL × 1 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions CRYSTALS FORMED FROM 1 TO 1 OF RESERVOIR SOLUTION (1.8 M AMMONIUM SULFATE, 50 MM COCL2 AND 100 MM MES PH 6.5) AND PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL (PH 8.0), AND 50 MM NACL).	Resolution 2.40 Å R-free 0.313
2XRE Detection of cobalt in previously unassigned human SENP1 structure Deposited 2010-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 415–644（230 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644 Chain B 415–644（230 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	Not recorded	GOL GLYCEROL × 10 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；CRYSTALLIZATION WAS PERFORMED USING A SITTING-DROP VAPOUR-DIFFUSION METHOD. CRYSTALS APPEARED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL, PH 8.0, AND 50 MM NACL) AND RESERVOIR SOLUTION CONTAINING 100 MM COCL2, 0.1M MES, PH 6.5, AND 1.8 M (NH4)2SO4.	Resolution 2.45 Å R-free 0.317
2XRE Detection of cobalt in previously unassigned human SENP1 structure Deposited 2010-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 415–644（230 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644 Chain B 415–644（230 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	Not recorded	GOL GLYCEROL × 10 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；CRYSTALLIZATION WAS PERFORMED USING A SITTING-DROP VAPOUR-DIFFUSION METHOD. CRYSTALS APPEARED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL, PH 8.0, AND 50 MM NACL) AND RESERVOIR SOLUTION CONTAINING 100 MM COCL2, 0.1M MES, PH 6.5, AND 1.8 M (NH4)2SO4.	Resolution 2.45 Å R-free 0.317
2XRE Detection of cobalt in previously unassigned human SENP1 structure Deposited 2010-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 415–644（230 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；CRYSTALLIZATION WAS PERFORMED USING A SITTING-DROP VAPOUR-DIFFUSION METHOD. CRYSTALS APPEARED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL, PH 8.0, AND 50 MM NACL) AND RESERVOIR SOLUTION CONTAINING 100 MM COCL2, 0.1M MES, PH 6.5, AND 1.8 M (NH4)2SO4.	Resolution 2.45 Å R-free 0.317
2XRE Detection of cobalt in previously unassigned human SENP1 structure Deposited 2010-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 415–644（230 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	Not recorded	GOL GLYCEROL × 6 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；CRYSTALLIZATION WAS PERFORMED USING A SITTING-DROP VAPOUR-DIFFUSION METHOD. CRYSTALS APPEARED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL, PH 8.0, AND 50 MM NACL) AND RESERVOIR SOLUTION CONTAINING 100 MM COCL2, 0.1M MES, PH 6.5, AND 1.8 M (NH4)2SO4.	Resolution 2.45 Å R-free 0.317
6NNQ Non-covalent structure of SENP1 in complex with SUMO2 Deposited 2019-01-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 421–643（223 aa） Fragment：residues 421-643	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

9 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SENP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–174； UniProt 419–592 Author chain A； PDBConstruct 176–226； UniProt 593–643

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 15–95	Fragment：CATALYTIC FRAGMENT, RESIDUES 15-95	SENTRIN-SPECIFIC PROTEASE 1 × 1 （Q9P0U3）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.20 Å R-free 0.288

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 2IYD	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 construct 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 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 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
2IO3 Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2 Deposited 2006-10-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 15–93（79 aa）	Not recorded	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
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 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 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 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 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 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 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 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 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 1–81； UniProt 15–95

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	2iyd
Deposition date deposition_date	2006-07-14
Structure title title	SENP1 covalent complex with SUMO-2
Keywords keywords	PROTEASE, HYDROLASE, THIOL PROTEASE, NUCLEAR PROTEIN, UBL CONJUGATION PATHWAY; 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	21.15 Å
Radius of gyration Rg (electron density) rg_electron	20.00 Å
Forward intensity I(0) i0	22379700.00
Molecular weight molecular_weight	35930.0 kDa
Excluded volume excluded_volume	44985 Å³
Envelope volume envelope_volume	52987 Å³
Hydration-shell volume shell_volume	21918 Å³
Envelope diameter envelope_diameter	69.2 Å
Shell Rg shell_rg	26.85 Å
Envelope Rg envelope_rg	20.35 Å
Shape Rg shape_rg	19.99 Å
Total Rg total_rg	20.97 Å
Total atoms total_atoms	2524
Residues n_residues	305
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	68.7 Å
Rg (real space) rg_real	21.05 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.2380e+07
I(0) uncertainty (real space) i0_real_error	2.9590e+05
Rg (reciprocal space) rg_reciprocal	21.07 Å
I(0) (reciprocal space) i0_reciprocal	22380000.0000
Solution quality estimate total_estimate	0.8907
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.223
Kurtosis Kurtosis kurtosis	-0.409
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5291000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	SENTRIN-SPECIFIC PROTEASE 1
Molecular weight formula_weight	26932.2 kDa
EC 编号 ec_number	3.4.22.-
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	2524

EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

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	9325.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVY

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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2iydb1
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 (2 domains)

Domain ID domain_id	2iydA00
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	2iydB00
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

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8. Citations (2)

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Unit-cell length a length_a	143.376 Å
Unit-cell length b length_b	143.376 Å
Unit-cell length c length_c	71.886 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	46.980 Å
R factor r_factor	0.2730
R_work r_work	0.2720
R_free r_free	0.2880

fit	/app/data/saxs_computation/iy/2iyd/2iyd.fit
pddf	/app/data/pr_computation/iy/2iyd/2iyd.pr.out
profile	/app/data/saxs_computation/iy/2iyd/2iyd.dat

SENP1 covalent complex with SUMO-2

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

SENTRIN-SPECIFIC PROTEASE 1

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

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)