SAXSdb — 3pyc

▼

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 13–140	Fragment：C2 domain, UNP residues 13-140	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

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 3PYC	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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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
2LTX Smurf1 WW2 domain in complex with a Smad7 derived peptide Deposited 2012-06-04	Different construct Different oligomeric state 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 306–340（35 aa） Fragment：WW2 domain (UNP residues 306-340)	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 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
9FSJ Crystal structure of the HECT domain of Smurf 1 in complex with inhibitor 8 Deposited 2024-06-21	Different construct Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 5–132； UniProt 13–140

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3pyc
Deposition date deposition_date	2010-12-13
Structure title title	Crystal structure of human SMURF1 C2 domain
Keywords keywords	phospholipid binding, membrane associate, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.12 Å
Radius of gyration Rg (electron density) rg_electron	15.04 Å
Forward intensity I(0) i0	4520780.00
Molecular weight molecular_weight	14977.0 kDa
Excluded volume excluded_volume	18700 Å³
Envelope volume envelope_volume	21432 Å³
Hydration-shell volume shell_volume	12397 Å³
Envelope diameter envelope_diameter	60.5 Å
Shell Rg shell_rg	20.41 Å
Envelope Rg envelope_rg	15.53 Å
Shape Rg shape_rg	15.06 Å
Total Rg total_rg	16.06 Å
Total atoms total_atoms	1049
Residues n_residues	132
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	62.3 Å
Rg (real space) rg_real	16.08 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	4.5210e+06
I(0) uncertainty (real space) i0_real_error	6.0400e+04
Rg (reciprocal space) rg_reciprocal	16.09 Å
I(0) (reciprocal space) i0_reciprocal	4521000.0000
Solution quality estimate total_estimate	0.7957
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.167
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	794100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.503; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase SMURF1
Molecular weight formula_weight	14841.1 kDa
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	1113

GSEFIKIRLTVLCAKNLAKKDFFRLPDPFAKIVVDGSGQCHSTDTVKNTLDPKWNQHYDLYVGKTDSITISVWNHKKIHKKQGAGFLGCVRLLSNAISRLKDTGYQRLDLCKLNPSDTDAVRGQIVVSLQTR

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	54

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3pycA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	30.959 Å
Unit-cell length b length_b	47.048 Å
Unit-cell length c length_c	91.266 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	4

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

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	32.760 Å
R factor r_factor	0.2058
R_work r_work	0.2041
R_free r_free	0.2412

fit	/app/data/saxs_computation/py/3pyc/3pyc.fit
pddf	/app/data/pr_computation/py/3pyc/3pyc.pr.out
profile	/app/data/saxs_computation/py/3pyc/3pyc.dat

Crystal structure of human SMURF1 C2 domain

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

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