SAXSdb — 2ltx

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

E3 ubiquitin-protein ligase SMURF1

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 306–340	Fragment：WW2 domain (UNP residues 306-340)	Smad7 derived peptide × 1 （O15105）	SOLUTION NMR NMR measurement conditions：pH 7.2；285 K；Pressure ambient NMR sample composition：1 mM SMURF1WW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：1 mM [U-100% 13C; U-100% 15N] SMURF1WW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2LTX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LAZ Structure of the first WW domain of human Smurf1 in complex with a mono-phosphorylated human Smad1 derived peptide Deposited 2011-03-22	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 235–267（33 aa） Fragment：residues 235-267	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LB0 Structure of the first WW domain of human Smurf1 in complex with a di-phosphorylated human Smad1 derived peptide Deposited 2011-03-22	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 235–267（33 aa） Fragment：residues 235-267	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient NMR sample composition 1 mM NEDD4LWW3-1, 3 mM SMAD3-2, 20 mM sodium phosphate-3, 100 mM sodium chloride-4, 2 mM sodium azide-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3-6, 3 mM SMAD3-7, 20 mM sodium phosphate-8, 100 mM sodium chloride-9, 2 mM sodium azide-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3-11, 3 mM SMAD3-12, 20 mM sodium phosphate-13, 100 mM sodium chloride-14, 2 mM sodium azide-15, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LB1 Structure of the second domain of human Smurf1 in complex with a human Smad1 derived peptide Deposited 2011-03-22	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 305–340（36 aa） Fragment：residues 305-339	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3PYC Crystal structure of human SMURF1 C2 domain Deposited 2010-12-13	Different construct 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 13–140（128 aa） Fragment：C2 domain, UNP residues 13-140	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M HEPES (pH 6.5), 2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.96 Å R-free 0.241
9FSJ Crystal structure of the HECT domain of Smurf 1 in complex with inhibitor 8 Deposited 2024-06-21	Different construct 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 377–751（375 aa）	Not recorded	TJQ ethyl 5-[1,3-benzodioxol-5-ylmethyl(ethyl)carbamoyl]-2,4-dimethyl-1~{H}-pyrrole-3-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG1500, 100 mM SPG pH 9	Resolution 2.05 Å R-free 0.279
9FSK Crystal structure of the HECT domain of Smurf1 Deposited 2024-06-21	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 377–751（375 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25 % PEG 3350, 0.1 M Bis Tris pH 5.9, 0.2 M MgCl2, 0.02 M NH4OAc	Resolution 2.75 Å R-free 0.301
9FSK Crystal structure of the HECT domain of Smurf1 Deposited 2024-06-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 377–751（375 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25 % PEG 3350, 0.1 M Bis Tris pH 5.9, 0.2 M MgCl2, 0.02 M NH4OAc	Resolution 2.75 Å R-free 0.301
9FSK Crystal structure of the HECT domain of Smurf1 Deposited 2024-06-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 377–751（375 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25 % PEG 3350, 0.1 M Bis Tris pH 5.9, 0.2 M MgCl2, 0.02 M NH4OAc	Resolution 2.75 Å R-free 0.301
9FSK Crystal structure of the HECT domain of Smurf1 Deposited 2024-06-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 377–751（375 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25 % PEG 3350, 0.1 M Bis Tris pH 5.9, 0.2 M MgCl2, 0.02 M NH4OAc	Resolution 2.75 Å R-free 0.301

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

View Construct and Data Evidence

UniProt name	SMUF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–35； UniProt 306–340

Smad7 derived peptide

OrganismNot specified

UniProt O15105

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 203–217	Fragment：UNP residues 203-217	E3 ubiquitin-protein ligase SMURF1 × 1 （Q9HCE7）	SOLUTION NMR NMR measurement conditions：pH 7.2；285 K；Pressure ambient NMR sample composition：1 mM SMURF1WW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：1 mM [U-100% 13C; U-100% 15N] SMURF1WW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2LTX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DJY Solution structure of Smurf2 WW3 domain-Smad7 PY peptide complex Deposited 2006-04-06	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 203–217（15 aa） Fragment：PY motif region	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Pressure 1	Resolution not provided
2LTV YAP WW2 in complex with a Smad7 derived peptide Deposited 2012-06-04	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 206–217（12 aa） Fragment：UNP residues 206-217	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；285 K；Pressure ambient NMR sample composition 1 mM YAPWW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] YAPWW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LTW YAP WW1 in complex with a Smad7 derived peptide Deposited 2012-06-04	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 205–217（13 aa） Fragment：UNP residues 205-217	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；285 K；Pressure ambient NMR sample composition 1 mM YAPWW1, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] YAPWW1, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LTY NEDD4L WW2 domain in complex with a Smad7 derived peptide Deposited 2012-06-04	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 203–217（15 aa） Fragment：UNP residues 203-217	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；285 K；Pressure ambient NMR sample composition 1 mM NEDD4LWW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LTZ Smurf2 WW3 domain in complex with a Smad7 derived peptide Deposited 2012-06-04	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 203–217（15 aa） Fragment：UNP residues 203-217	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；285 K；Pressure ambient NMR sample composition 1 mM SMURF2WW3, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] SMURF2WW3, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SMAD7_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–15； UniProt 203–217

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	2ltx
Deposition date deposition_date	2012-06-04
Structure title title	Smurf1 WW2 domain in complex with a Smad7 derived peptide
Keywords keywords	WW, SMURF1, SMAD7, PROTEIN BINDING-PEPTIDE complex; PROTEIN BINDING/PEPTIDE
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	10.90 Å
Radius of gyration Rg (electron density) rg_electron	10.84 Å
Forward intensity I(0) i0	314961000.00
Molecular weight molecular_weight	145710.0 kDa
Excluded volume excluded_volume	180120 Å³
Envelope volume envelope_volume	13662 Å³
Hydration-shell volume shell_volume	9623 Å³
Envelope diameter envelope_diameter	39.5 Å
Shell Rg shell_rg	17.73 Å
Envelope Rg envelope_rg	12.66 Å
Shape Rg shape_rg	10.78 Å
Total Rg total_rg	11.20 Å
Total atoms total_atoms	20075
Residues n_residues	1250
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	35.4 Å
Rg (real space) rg_real	10.82 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	3.1500e+08
I(0) uncertainty (real space) i0_real_error	3.3140e+06
Rg (reciprocal space) rg_reciprocal	10.82 Å
I(0) (reciprocal space) i0_reciprocal	315000000.0000
Solution quality estimate total_estimate	0.7392
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	13.4 Å
Skewness Skewness skewness	-0.012
Kurtosis Kurtosis kurtosis	-0.541
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	47680.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.998; Smooth: 0.953

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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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8. Citations (1)

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Description description	E3 ubiquitin-protein ligase SMURF1
Molecular weight formula_weight	4057.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	20075

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	Smad7 derived peptide
Molecular weight formula_weight	1779.0 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/lt/2ltx/2ltx.fit
pddf	/app/data/pr_computation/lt/2ltx/2ltx.pr.out
profile	/app/data/saxs_computation/lt/2ltx/2ltx.dat

Smurf1 WW2 domain in complex with a Smad7 derived peptide

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

E3 ubiquitin-protein ligase SMURF1

State in the Current Structure

Other States of the Same Protein in the Database

Smad7 derived peptide

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)