SAXSdb — 5odg

▼

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

Mothers against decapentaplegic homolog 3

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 11–135 Chain B； UniProt 11–135	Fragment：MH1 domain, UNP residues 11-135	;DNA (5'-D(PCPAPGPGPCPTPAPGPCPCPTPGPCPA)-3') ; × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.02 M sodium potassium phosphate, 0.1 M BisTris propane pH 6.5, 20% PEG 3350	Resolution 2.12 Å R-free 0.242
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 11–135 Chain B； UniProt 11–135	Fragment：MH1 domain, UNP residues 11-135	;DNA (5'-D(PCPAPGPGPCPTPAPGPCPCPTPGPCPA)-3') ; × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.02 M sodium potassium phosphate, 0.1 M BisTris propane pH 6.5, 20% PEG 3350	Resolution 2.12 Å R-free 0.242

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 5ODG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MHD CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA Deposited 1998-08-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–132（132 aa） Fragment：MH1 DOMAIN, RESIDUES 1 - 144 Chain B 1–132（132 aa） Fragment：MH1 DOMAIN, RESIDUES 1 - 144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.80 Å R-free 0.288
1MJS MH2 domain of transcriptional factor SMAD3 Deposited 2002-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 229–425（197 aa） Fragment：MH2 domain, residues 229-425	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.91 Å R-free 0.199
1MK2 SMAD3 SBD complex Deposited 2002-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 220–425（206 aa） Fragment：MH2 domain, residues 220-425	Not recorded	ACY ACETIC ACID × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.74 Å R-free 0.271
1MK2 SMAD3 SBD complex Deposited 2002-08-28	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 A 220–425（206 aa） Fragment：MH2 domain, residues 220-425	Not recorded	ACY ACETIC ACID × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.74 Å R-free 0.271
1OZJ Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution Deposited 2003-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–144（144 aa） Fragment：DWA DOMAIN Chain B 1–144（144 aa） Fragment：DWA DOMAIN	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；citrate, PEG2000, ammonium acetate, spermine, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.270
1U7F Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex Deposited 2004-08-03	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 228–424（197 aa） Fragment：MH2 and Linker domains Chain C 228–424（197 aa） Fragment：MH2 and Linker domains	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；50 mM Tris-HCl, 0-15 mM magnesium chloride, 5-15% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.247
2LAJ Third WW domain of human Nedd4L in complex with doubly phosphorylated human smad3 derived peptide Deposited 2011-03-16	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 × 2 PDB declaration: dimeric	Chain B 202–211（10 aa） Fragment：sequence database residues 202-211	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
2LB2 Structure of the second domain of human Nedd4L in complex with a phosphorylated pTPY motif derived from human Smad3 Deposited 2011-03-22	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 × 2 PDB declaration: dimeric	Chain B 178–189（12 aa） Fragment：residues 178-189	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
5OD6 Crystal structure of Smad3-MH1 bound to the GGCGC site. Deposited 2017-07-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 11–135（125 aa） Chain B 11–135（125 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M lithium acetate, 20% PEG 3350	Resolution 2.00 Å R-free 0.235
5XOC Crystal structure of human Smad3-FoxH1 complex Deposited 2017-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 220–416（197 aa） Fragment：UNP residues 220-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；0.1 M citrate pH 5.4, 0.8% ethylene imine polymer and 0.5 M NaCl	Resolution 2.40 Å R-free 0.235
6ZMN Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site Deposited 2020-07-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 10–136（127 aa） Chain B 10–136（127 aa）	Not recorded	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2 M sodium acetate	Resolution 2.33 Å R-free 0.252

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

View Construct and Data Evidence

UniProt name	SMAD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–128； UniProt 11–135 Author chain B； PDBConstruct 4–128； UniProt 11–135

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	5odg
Deposition date deposition_date	2017-07-05
Structure title title	Crystal structure of Smad3-MH1 bound to the GGCT site.
Keywords keywords	Smads, transcription factor, DNA complex, transcription; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.95 Å
Radius of gyration Rg (electron density) rg_electron	24.10 Å
Forward intensity I(0) i0	31073800.00
Molecular weight molecular_weight	37094.0 kDa
Excluded volume excluded_volume	43964 Å³
Envelope volume envelope_volume	58646 Å³
Hydration-shell volume shell_volume	21412 Å³
Envelope diameter envelope_diameter	89.9 Å
Shell Rg shell_rg	29.90 Å
Envelope Rg envelope_rg	23.95 Å
Shape Rg shape_rg	23.99 Å
Total Rg total_rg	25.01 Å
Total atoms total_atoms	2562
Residues n_residues	277
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	86.7 Å
Rg (real space) rg_real	25.09 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	3.1070e+07
I(0) uncertainty (real space) i0_real_error	5.1040e+05
Rg (reciprocal space) rg_reciprocal	25.06 Å
I(0) (reciprocal space) i0_reciprocal	31070000.0000
Solution quality estimate total_estimate	0.7863
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.445
Kurtosis Kurtosis kurtosis	-0.325
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2595000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.789; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Mothers against decapentaplegic homolog 3
Molecular weight formula_weight	15036.6 kDa
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	2643

GAMIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVETPVL

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	;DNA (5'-D(PCPAPGPGPCPTPAPGPCPCPTPGPCPA)-3') ;
Molecular weight formula_weight	4899.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,E

TGCAGGCTAGCCTGCA

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5odgA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	520 — Smad3; Chain A
Homologous superfamily homologous superfamily	10 — SMAD MH1 domain

Domain ID domain_id	5odgB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	520 — Smad3; Chain A
Homologous superfamily homologous superfamily	10 — SMAD MH1 domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	104.990 Å
Unit-cell length b length_b	104.990 Å
Unit-cell length c length_c	72.490 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	16

Space group space_group	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.120 Å
Low-resolution limit resolution_low	29.830 Å
R factor r_factor	0.2020
R_work r_work	0.1990
R_free r_free	0.2420

fit	/app/data/saxs_computation/od/5odg/5odg.fit
pddf	/app/data/pr_computation/od/5odg/5odg.pr.out
profile	/app/data/saxs_computation/od/5odg/5odg.dat

Crystal structure of Smad3-MH1 bound to the GGCT site.

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

Mothers against decapentaplegic homolog 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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)