SAXSdb — 1th0

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 364–589	Fragment：catalytic domain	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 364–589	Fragment：catalytic domain	No other associated polymer	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

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 1TH0	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 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 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
2IO0 Crystal structure of human Senp2 in complex with preSUMO-2 Deposited 2006-10-09	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	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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 21 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 1–226； UniProt 364–589 Author chain B； PDBConstruct 1–226； UniProt 364–589

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	1th0
Deposition date deposition_date	2004-05-31
Structure title title	Structure of human Senp2
Keywords keywords	SUMO; AXAM; SENP; ULP; PROTEASE, CELL CYCLE, HYDROLASE; CELL CYCLE, 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	29.80 Å
Radius of gyration Rg (electron density) rg_electron	29.15 Å
Forward intensity I(0) i0	44080300.00
Molecular weight molecular_weight	53160.0 kDa
Excluded volume excluded_volume	67130 Å³
Envelope volume envelope_volume	83734 Å³
Hydration-shell volume shell_volume	25007 Å³
Envelope diameter envelope_diameter	97.5 Å
Shell Rg shell_rg	34.79 Å
Envelope Rg envelope_rg	28.94 Å
Shape Rg shape_rg	29.15 Å
Total Rg total_rg	29.74 Å
Total atoms total_atoms	3744
Residues n_residues	449
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	95.3 Å
Rg (real space) rg_real	29.94 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	4.4080e+07
I(0) uncertainty (real space) i0_real_error	7.0610e+05
Rg (reciprocal space) rg_reciprocal	29.89 Å
I(0) (reciprocal space) i0_reciprocal	44080000.0000
Solution quality estimate total_estimate	0.8560
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.336
Kurtosis Kurtosis kurtosis	-0.781
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10750000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.805; Smooth: 0.889

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1th0a_
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	d1th0b_
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

CATH v4.4 (2 domains)

Domain ID domain_id	1th0A00
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	1th0B00
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

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8. Citations (1)

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Unit-cell length a length_a	123.237 Å
Unit-cell length b length_b	59.228 Å
Unit-cell length c length_c	94.015 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	19.460 Å
R factor r_factor	0.2110
R_work r_work	0.2100
R_free r_free	0.2470

Description description	Sentrin-specific protease 2
Molecular weight formula_weight	26787.1 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3953

Structure of human Senp2

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

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 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

fit	/app/data/saxs_computation/th/1th0/1th0.fit
pddf	/app/data/pr_computation/th/1th0/1th0.pr.out
profile	/app/data/saxs_computation/th/1th0/1th0.dat