SAXSdb — 2xre

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 415–644 Chain B； UniProt 415–644	Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 415–644 Chain B； UniProt 415–644	Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 415–644	Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 415–644	Fragment：CATALYTIC FRAGMENT, RESIDUES 415-644	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

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 2XRE	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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 ligand/ion Different experimental conditions 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
2IYD SENP1 covalent complex with SUMO-2 Deposited 2006-07-14	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 A 419–592（174 aa） Fragment：CATALYTIC FRAGMENT, RESIDUES 419-643 Chain A 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 3.20 Å R-free 0.288
2XPH Crystal structure of human SENP1 with the bound cobalt Deposited 2010-08-26	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 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
6NNQ Non-covalent structure of SENP1 in complex with SUMO2 Deposited 2019-01-15	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 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 13 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 1–230； UniProt 415–644 Author chain B； PDBConstruct 1–230； UniProt 415–644

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	2xre
Deposition date deposition_date	2010-09-14
Structure title title	Detection of cobalt in previously unassigned human SENP1 structure
Keywords keywords	HYDROLASE, CYSTEINE PROTEASE; 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	25.42 Å
Radius of gyration Rg (electron density) rg_electron	24.34 Å
Forward intensity I(0) i0	46946500.00
Molecular weight molecular_weight	53630.0 kDa
Excluded volume excluded_volume	67343 Å³
Envelope volume envelope_volume	82220 Å³
Hydration-shell volume shell_volume	27903 Å³
Envelope diameter envelope_diameter	83.4 Å
Shell Rg shell_rg	31.63 Å
Envelope Rg envelope_rg	24.50 Å
Shape Rg shape_rg	24.33 Å
Total Rg total_rg	25.23 Å
Total atoms total_atoms	3766
Residues n_residues	453
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	80.9 Å
Rg (real space) rg_real	25.35 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	4.6950e+07
I(0) uncertainty (real space) i0_real_error	6.4920e+05
Rg (reciprocal space) rg_reciprocal	25.38 Å
I(0) (reciprocal space) i0_reciprocal	46950000.0000
Solution quality estimate total_estimate	0.9051
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.233
Kurtosis Kurtosis kurtosis	-0.533
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12820000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; 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 (4)

Entity 1 Entity 1 polymer

Description description	SENTRIN-SPECIFIC PROTEASE 1
Molecular weight formula_weight	27378.6 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	3952

DSEDEFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

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 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2xrea_
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	d2xreb_
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	2xreA00
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	2xreB00
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	71.981 Å
Unit-cell length b length_b	71.981 Å
Unit-cell length c length_c	200.640 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	45.600 Å
R factor r_factor	0.2410
R_work r_work	0.2370
R_free r_free	0.3170

fit	/app/data/saxs_computation/xr/2xre/2xre.fit
pddf	/app/data/pr_computation/xr/2xre/2xre.pr.out
profile	/app/data/saxs_computation/xr/2xre/2xre.dat

Detection of cobalt in previously unassigned human SENP1 structure

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

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