SAXSdb — 1mk2

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

SMAD 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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 220–425	Fragment：MH2 domain, residues 220-425	Madh-interacting protein × 2 （O95405） ACY ACETIC ACID × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.74 Å R-free 0.271
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 220–425	Fragment：MH2 domain, residues 220-425	Madh-interacting protein × 1 （O95405） ACY ACETIC ACID × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.74 Å R-free 0.271

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 1MK2	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 mutation/modification Different oligomeric state 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 oligomeric state Different ligand/ion 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
1OZJ Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution Deposited 2003-04-09	Different construct Different mutation/modification Different oligomeric state 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 mutation/modification 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 1–206； UniProt 220–425

Madh-interacting protein

Homo sapiens

UniProt O95405

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 773–810	Fragment：SARA SBD domain, residues 773-810	SMAD 3 × 2 （P84022） ACY ACETIC ACID × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.74 Å R-free 0.271
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 773–810	Fragment：SARA SBD domain, residues 773-810	SMAD 3 × 1 （P84022） ACY ACETIC ACID × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.74 Å R-free 0.271

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 1MK2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DEV CRYSTAL STRUCTURE OF SMAD2 MH2 DOMAIN BOUND TO THE SMAD-BINDING DOMAIN OF SARA Deposited 1999-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 669–709（41 aa） Fragment：SARA SMAD2-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；TRIS, DIOXANE, AMMONIUM SULFATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.20 Å R-free 0.276
1DEV CRYSTAL STRUCTURE OF SMAD2 MH2 DOMAIN BOUND TO THE SMAD-BINDING DOMAIN OF SARA Deposited 1999-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 669–709（41 aa） Fragment：SARA SMAD2-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；TRIS, DIOXANE, AMMONIUM SULFATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.20 Å R-free 0.276
4BKW Crystal structure of the C-terminal region of human ZFYVE9 Deposited 2013-04-30	Different construct 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 895–1425（531 aa） Fragment：PROTEIN INTERACTING DOMAIN, RESIDUES 895-1425	Not recorded	EDO 1,2-ETHANEDIOL × 5 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M BIS-TRIS PH 6.5, 0.15M MAGNESIUM CHLORIDE, 30% PEG 3350	Resolution 2.53 Å R-free 0.247
5MJY Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (SARA complex structure) Deposited 2016-12-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–22（22 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M MMT buffer pH 9.0, 25% PEG1500	Resolution 2.25 Å R-free 0.235
5MJY Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (SARA complex structure) Deposited 2016-12-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–22（22 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M MMT buffer pH 9.0, 25% PEG1500	Resolution 2.25 Å R-free 0.235

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

View Construct and Data Evidence

UniProt name	ZFYV9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–38； UniProt 773–810

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	1mk2
Deposition date deposition_date	2002-08-28
Structure title title	SMAD3 SBD complex
Keywords keywords	SMAD3, SBD, SARA, TRANSCRIPTION; TRANSCRIPTION
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	18.87 Å
Radius of gyration Rg (electron density) rg_electron	17.83 Å
Forward intensity I(0) i0	12891600.00
Molecular weight molecular_weight	26330.0 kDa
Excluded volume excluded_volume	32670 Å³
Envelope volume envelope_volume	36198 Å³
Hydration-shell volume shell_volume	17229 Å³
Envelope diameter envelope_diameter	64.5 Å
Shell Rg shell_rg	23.90 Å
Envelope Rg envelope_rg	18.22 Å
Shape Rg shape_rg	17.81 Å
Total Rg total_rg	18.77 Å
Total atoms total_atoms	1848
Residues n_residues	235
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	62.7 Å
Rg (real space) rg_real	18.82 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.2890e+07
I(0) uncertainty (real space) i0_real_error	1.7380e+05
Rg (reciprocal space) rg_reciprocal	18.83 Å
I(0) (reciprocal space) i0_reciprocal	12890000.0000
Solution quality estimate total_estimate	0.8018
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.296
Kurtosis Kurtosis kurtosis	-0.249
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2228000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SMAD 3
Molecular weight formula_weight	23227.4 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	1848

DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNSERFCLGLLSNVNRNAAVELTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS

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	Madh-interacting protein
Molecular weight formula_weight	3818.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SPNPNNPAEYCSTIPPLQQAQASGALSSPPPTVMVPVG

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 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1mk2a_
Class class	b — All beta proteins
Fold Fold fold	b.26 — SMAD/FHA domain
Superfamily Superfamily superfamily	b.26.1 — SMAD/FHA domain
Family Family family	b.26.1.1 — SMAD domain

Domain ID domain_id	d1mk2b_
Class class	j — Peptides
Fold Fold fold	j.64 — Smad-binding domain of Sara
Superfamily Superfamily superfamily	j.64.1 — Smad-binding domain of Sara
Family Family family	j.64.1.1 — Smad-binding domain of Sara

CATH v4.4 (1 domains)

Domain ID domain_id	1mk2A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	49.995 Å
Unit-cell length b length_b	71.716 Å
Unit-cell length c length_c	86.886 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.740 Å
Low-resolution limit resolution_low	43.440 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2710

fit	/app/data/saxs_computation/mk/1mk2/1mk2.fit
pddf	/app/data/pr_computation/mk/1mk2/1mk2.pr.out
profile	/app/data/saxs_computation/mk/1mk2/1mk2.dat

SMAD3 SBD complex

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

SMAD 3

State in the Current Structure

Other States of the Same Protein in the Database

Madh-interacting protein

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)