SAXSdb — 9gnn

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

Sentrin-specific protease 5

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 568–755	Not recorded	Small ubiquitin-related modifier 3 × 1 （P55854） AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000	Resolution 2.36 Å R-free 0.283
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 568–755	Not recorded	Small ubiquitin-related modifier 3 × 1 （P55854） AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000	Resolution 2.36 Å R-free 0.283

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 9GNN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9GNV Human SENP5 in complex with SUMO1 Deposited 2024-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 568–755（188 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；2.1 M Malic Ac., pH 7.0	Resolution 2.18 Å R-free 0.259
9GNX Human SENP5 in complex with SUMO1 (E67D) Deposited 2024-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 568–755（188 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M LiSO4, 8% PEG2000, 8% PEG500MME, 0.1 M NaAcetate pH 5.5	Resolution 1.90 Å R-free 0.258

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SENP5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–207； UniProt 568–755 Author chain B； PDBConstruct 20–207； UniProt 568–755

Small ubiquitin-related modifier 3

Homo sapiens

UniProt P55854

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 14–91	Not recorded	Sentrin-specific protease 5 × 1 （Q96HI0） AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000	Resolution 2.36 Å R-free 0.283
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 14–91	Not recorded	Sentrin-specific protease 5 × 1 （Q96HI0） AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000	Resolution 2.36 Å R-free 0.283

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 9GNN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U4A Solution structure of human SUMO-3 C47S Deposited 2004-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–92（79 aa） Fragment：ubiquitin-like domain	Mutation：C47S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.25；298 K；Ionic strength (raw mmCIF value) 25mM phosphate buffer, 75mM Nacl；Pressure 1 NMR sample composition 0.8mM 15N-labeled protein \| 25mM phosphate buffer, 75mM Nacl 90% H2O, 10% D2O NMR sample composition 0.6mM 13C,15N-labeled protein \| 25mM phosphate buffer, 75mM Nacl 90% H2O, 10% D2O	Resolution not provided
2IO1 Crystal structure of human Senp2 in complex with preSUMO-3 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 14–103（90 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；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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 14–103（90 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；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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 14–103（90 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；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
2MP2 Solution structure of SUMO dimer in complex with SIM2-3 from RNF4 Deposited 2014-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 12–92（81 aa） Fragment：UNP residues 12-92 Chain B 2–90（89 aa） Fragment：UNP residues 2-90	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6K5R Complex of SUMO2 with Phosphorylated viral SIM IE2 Deposited 2019-05-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 15–91（77 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 162.7；Pressure 1 NMR sample composition 0.3 mM [U-15N] SUMO2, 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] SUMO2, 1.5 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6NNQ Non-covalent structure of SENP1 in complex with SUMO2 Deposited 2019-01-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 15–92（78 aa） Fragment：residues 15-92	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；20% PEG 6000, 0.1M HEPES, pH 7.5	Resolution 2.62 Å R-free 0.277
7R2E Structure of human Senp7 with SUMO2 Deposited 2022-02-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 16–91（76 aa）	Not recorded	AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium HEPES 7.0, 15 % w/v PEG 20,000	Resolution 1.74 Å R-free 0.230
7R2E Structure of human Senp7 with SUMO2 Deposited 2022-02-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 16–91（76 aa）	Not recorded	AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium HEPES 7.0, 15 % w/v PEG 20,000	Resolution 1.74 Å R-free 0.230
7ZJU Structure of human USPL1 in covalent complex with SUMO3-2Br probe Deposited 2022-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–91（90 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1 OXU 2-bromanylethanamine × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100 mM Tris pH 8.8, 19% PEG6000, 200 mM CaCl2	Resolution 2.17 Å R-free 0.238
7ZJU Structure of human USPL1 in covalent complex with SUMO3-2Br probe Deposited 2022-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–91（90 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 2 OXU 2-bromanylethanamine × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100 mM Tris pH 8.8, 19% PEG6000, 200 mM CaCl2	Resolution 2.17 Å R-free 0.238

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SUMO3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–79； UniProt 14–91 Author chain D； PDBConstruct 2–79； UniProt 14–91

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	9gnn
Deposition date deposition_date	2024-09-03
最后修订 last_revision	2025-07-16
Structure title title	Structure of SENP5 in complex with SUMO2
Keywords keywords	SUMO, cysteine protease, SENP family, HYDROLASE; 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	25.75 Å
Radius of gyration Rg (electron density) rg_electron	24.62 Å
Forward intensity I(0) i0	64838100.00
Molecular weight molecular_weight	62741.0 kDa
Excluded volume excluded_volume	78619 Å³
Envelope volume envelope_volume	95056 Å³
Hydration-shell volume shell_volume	31308 Å³
Envelope diameter envelope_diameter	77.8 Å
Shell Rg shell_rg	32.55 Å
Envelope Rg envelope_rg	24.68 Å
Shape Rg shape_rg	24.56 Å
Total Rg total_rg	25.70 Å
Total atoms total_atoms	4404
Residues n_residues	534
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	76.3 Å
Rg (real space) rg_real	25.60 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	6.4840e+07
I(0) uncertainty (real space) i0_real_error	8.6510e+05
Rg (reciprocal space) rg_reciprocal	25.65 Å
I(0) (reciprocal space) i0_reciprocal	64840000.0000
Solution quality estimate total_estimate	0.9127
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.5 Å
Skewness Skewness skewness	0.127
Kurtosis Kurtosis kurtosis	-0.530
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20580000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Sentrin-specific protease 5
Molecular weight formula_weight	24420.3 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4428

HHHHHHSSGLVPRGSHMASMLDMDDLATLDGQNWLNDQVINMYGELIMDAVPDKVHFFNSFFHRQLVTKGYNGVKRWTKKVDLFKKSLLLIPIHLEVHWSLITVTLSNRIISFYDSQGIHFKFCVENIRKYLLTEAREKNRPEFLQGWQTAVTKCIPQQKNDSDCGVFVLQYCKCLALEQPFQFSQEDMPRVRKRIYKELCECRLMD

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Small ubiquitin-related modifier 3
Molecular weight formula_weight	9137.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTG

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 non-polymer

Description description	prop-2-en-1-amine
Molecular weight formula_weight	57.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	24

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8. Citations (1)

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Unit-cell length a length_a	66.162 Å
Unit-cell length b length_b	87.902 Å
Unit-cell length c length_c	116.676 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.360 Å
Low-resolution limit resolution_low	48.610 Å
R factor r_factor	0.2165
R_work r_work	0.2130
R_free r_free	0.2826

fit	/app/data/saxs_computation/gn/9gnn/9gnn.fit
pddf	/app/data/pr_computation/gn/9gnn/9gnn.pr.out
profile	/app/data/saxs_computation/gn/9gnn/9gnn.dat

Structure of SENP5 in complex with SUMO2

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

Sentrin-specific protease 5

State in the Current Structure

Other States of the Same Protein in the Database

Small ubiquitin-related modifier 3

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)