SAXSdb — 1mhd

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

SMAD3

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 1–132 Chain B； UniProt 1–132	Fragment：MH1 DOMAIN, RESIDUES 1 - 144	DNA × 1 DNA × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6	Resolution 2.80 Å R-free 0.288

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 1MHD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MJS MH2 domain of transcriptional factor SMAD3 Deposited 2002-08-28	Different construct Different mutation/modification Different oligomeric state 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 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 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 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
5ODG Crystal structure of Smad3-MH1 bound to the GGCT site. Deposited 2017-07-05	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） Fragment：MH1 domain, UNP residues 11-135 Chain B 11–135（125 aa） Fragment：MH1 domain, UNP residues 11-135	Not recorded	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
5ODG Crystal structure of Smad3-MH1 bound to the GGCT site. Deposited 2017-07-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 11–135（125 aa） Fragment：MH1 domain, UNP residues 11-135 Chain B 11–135（125 aa） Fragment：MH1 domain, UNP residues 11-135	Not recorded	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
5XOC Crystal structure of human Smad3-FoxH1 complex Deposited 2017-05-27	Different construct Different mutation/modification Different oligomeric state 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 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SMAD3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 1–132 Author chain B； PDBConstruct 1–132； UniProt 1–132

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	1mhd
Deposition date deposition_date	1998-08-18
Structure title title	CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA
Keywords keywords	COMPLEX (TRANSCRIPTION ACTIVATOR-DNA), SMAD3 MH1, SMAD BINDING ELEMENT, DNA, COMPLEX (TRANSCRIPTION ACTIVATOR-DNA) complex; COMPLEX (TRANSCRIPTION ACTIVATOR/DNA)
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	23.64 Å
Radius of gyration Rg (electron density) rg_electron	23.87 Å
Forward intensity I(0) i0	30796600.00
Molecular weight molecular_weight	37332.0 kDa
Excluded volume excluded_volume	44544 Å³
Envelope volume envelope_volume	56844 Å³
Hydration-shell volume shell_volume	21118 Å³
Envelope diameter envelope_diameter	81.6 Å
Shell Rg shell_rg	29.36 Å
Envelope Rg envelope_rg	23.64 Å
Shape Rg shape_rg	23.90 Å
Total Rg total_rg	24.44 Å
Total atoms total_atoms	2590
Residues n_residues	273
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	81.2 Å
Rg (real space) rg_real	23.78 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	3.0800e+07
I(0) uncertainty (real space) i0_real_error	4.7880e+05
Rg (reciprocal space) rg_reciprocal	23.75 Å
I(0) (reciprocal space) i0_reciprocal	30800000.0000
Solution quality estimate total_estimate	0.8530
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.521
Kurtosis Kurtosis kurtosis	-0.201
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3001000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.979

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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	DNA
Molecular weight formula_weight	3959.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	2614

CAGTCTAGACATA

Entity 2 Entity 2 polymer

Description description	DNA
Molecular weight formula_weight	4294.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TATGTCTAGACTGA

Entity 3 Entity 3 polymer

Description description	SMAD3
Molecular weight formula_weight	15539.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MSSILPFTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVET

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 BL21(DE3)

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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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1mhda_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.164 — SMAD MH1 domain
Superfamily Superfamily superfamily	d.164.1 — SMAD MH1 domain
Family Family family	d.164.1.1 — SMAD MH1 domain

Domain ID domain_id	d1mhdb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.164 — SMAD MH1 domain
Superfamily Superfamily superfamily	d.164.1 — SMAD MH1 domain
Family Family family	d.164.1.1 — SMAD MH1 domain

CATH v4.4 (2 domains)

Domain ID domain_id	1mhdA00
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	1mhdB00
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

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8. Citations (1)

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Unit-cell length a length_a	45.600 Å
Unit-cell length b length_b	60.400 Å
Unit-cell length c length_c	71.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2880

fit	/app/data/saxs_computation/mh/1mhd/1mhd.fit
pddf	/app/data/pr_computation/mh/1mhd/1mhd.pr.out
profile	/app/data/saxs_computation/mh/1mhd/1mhd.dat

CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA

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

SMAD3

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)