SAXSdb — 5zoj

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

Mothers against decapentaplegic homolog 2

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 262–458 Chain B； UniProt 262–458 Chain C； UniProt 262–458	Fragment：UNP residues 262-458	Inner nuclear membrane protein Man1 × 2 （Q9Y2U8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；0.1M acetate, 7.5% PEG4000, 10% 2-propanol	Resolution 2.79 Å R-free 0.269

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 5ZOJ	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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 261–456（196 aa） Fragment：SMAD2 MH2 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 261–456（196 aa） Fragment：SMAD2 MH2 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
1KHX Crystal structure of a phosphorylated Smad2 Deposited 2001-12-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 241–467（227 aa）	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；293 K；dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.241
1U7V Crystal Structure of the phosphorylated Smad2/Smad4 heterotrimeric complex Deposited 2004-08-04	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 270–466（197 aa） Fragment：MH2 and Linker domains Chain C 270–466（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 2.70 Å R-free 0.279
2LB3 Structure of the WW domain of PIN1 in complex with a human phosphorylated Smad3 derived peptide 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 217–224（8 aa） Fragment：residues 176-183	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
5XOD Crystal structure of human Smad2-Ski complex Deposited 2017-05-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 262–458（197 aa） Fragment：UNP residues 262-458	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate tri-hydrate pH 4.6 and 1.85 M sodium formate	Resolution 1.85 Å R-free 0.254
6M64 Crystal structure of SMAD2 in complex with CBP Deposited 2020-03-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 262–464（203 aa） Chain C 262–464（203 aa） Chain E 262–464（203 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.1 M HEPES pH 7.2, 0.2 M NaCl and 31% PEG3350	Resolution 1.45 Å R-free 0.189
6ZVQ Complex between SMAD2 MH2 domain and peptide from Ski corepressor Deposited 2020-07-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 241–467（227 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 6 GOL GLYCEROL × 24 TAR D(-)-TARTARIC ACID × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；1.5M Ammonium Sulphate, 0.15M Sodium Potassium Tartrate, 0.08M Tri-Sodium Citrate pH 5.6, 25% v/v Glycerol	Resolution 2.03 Å R-free 0.210
7CO1 Crystal structure of SMAD2 in complex with wild-type CBP Deposited 2020-08-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 262–467（206 aa） Chain C 262–467（206 aa） Chain E 262–467（206 aa）	Mutation：S465E, S467E Mutation：S465E, S467E Mutation：S465E, S467E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；1 M sodium phosphate monobasic monohydrate-potassium phosphate dibasic	Resolution 3.30 Å R-free 0.283

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

View Construct and Data Evidence

UniProt name	SMAD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–200； UniProt 262–458 Author chain B； PDBConstruct 4–200； UniProt 262–458 Author chain C； PDBConstruct 4–200； UniProt 262–458

Inner nuclear membrane protein Man1

Homo sapiens

UniProt Q9Y2U8

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain D； UniProt 762–890 Chain E； UniProt 762–890	Fragment：UNP residues 762-890	Mothers against decapentaplegic homolog 2 × 3 （Q15796）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；0.1M acetate, 7.5% PEG4000, 10% 2-propanol	Resolution 2.79 Å R-free 0.269

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 5ZOJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CH0 Solution structure of the human MAN1 C-terminal domain (residues 655- 775) Deposited 2006-03-10	Different construct Different mutation/modification 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 655–775（121 aa） Fragment：655-775	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 MM PHOSPHATE, 150MM NACL NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 MM PHOSPHATE, 150MM NACL NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 MM PHOSPHATE, 150MM NACL NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 MM PHOSPHATE, 150MM NACL NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 MM PHOSPHATE, 150MM NACL NMR sample composition 90% H2O, 10% D2O	Resolution not provided
5ZOK Crystal structure of human SMAD1-MAN1 complex. Deposited 2018-04-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 762–890（129 aa） Fragment：UNP residues 762-890	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；0.1M MES, 10% PEG20,000	Resolution 2.85 Å R-free 0.255
5ZOK Crystal structure of human SMAD1-MAN1 complex. Deposited 2018-04-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 762–890（129 aa） Fragment：UNP residues 762-890	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；0.1M MES, 10% PEG20,000	Resolution 2.85 Å R-free 0.255

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

View Construct and Data Evidence

UniProt name	MAN1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 4–132； UniProt 762–890 Author chain E； PDBConstruct 4–132； UniProt 762–890

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	5zoj
Deposition date deposition_date	2018-04-13
Structure title title	Crystal structure of human SMAD2-MAN1 complex
Keywords keywords	Transcription, Complex, TGF-beta signaling, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	33.63 Å
Radius of gyration Rg (electron density) rg_electron	33.64 Å
Forward intensity I(0) i0	131693000.00
Molecular weight molecular_weight	90767.0 kDa
Excluded volume excluded_volume	113130 Å³
Envelope volume envelope_volume	145500 Å³
Hydration-shell volume shell_volume	38128 Å³
Envelope diameter envelope_diameter	122.8 Å
Shell Rg shell_rg	37.90 Å
Envelope Rg envelope_rg	34.10 Å
Shape Rg shape_rg	33.62 Å
Total Rg total_rg	34.03 Å
Total atoms total_atoms	6383
Residues n_residues	801
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	115.3 Å
Rg (real space) rg_real	33.80 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	1.3170e+08
I(0) uncertainty (real space) i0_real_error	2.3630e+06
Rg (reciprocal space) rg_reciprocal	33.70 Å
I(0) (reciprocal space) i0_reciprocal	131700000.0000
Solution quality estimate total_estimate	0.8552
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.3 Å
Skewness Skewness skewness	0.490
Kurtosis Kurtosis kurtosis	-0.275
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38070000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.818; Smooth: 0.887

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Mothers against decapentaplegic homolog 2
Molecular weight formula_weight	22518.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6383

GPGDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNATVEMTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGS

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	Inner nuclear membrane protein Man1
Molecular weight formula_weight	14970.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

GPGSKVWQGQAFHLDRRNSPPNSLTPCLKIRNMFDPVMEIGDQWHLAIQEAILEKCSDNDGIVHIAVDKNSREGCVYVKCLSPEYAGKAFKALHGSWFDGKLVTVKYLRLDRYHHRFPQALTSNTPLKPSNK

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

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5zoja_
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	d5zojb_
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	d5zojc_
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

CATH v4.4 (3 domains)

Domain ID domain_id	5zojA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5zojB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5zojC00
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	176.813 Å
Unit-cell length b length_b	176.813 Å
Unit-cell length c length_c	73.854 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.794 Å
Low-resolution limit resolution_low	42.469 Å
R factor r_factor	0.2433
R_work r_work	0.2419
R_free r_free	0.2692

fit	/app/data/saxs_computation/zo/5zoj/5zoj.fit
pddf	/app/data/pr_computation/zo/5zoj/5zoj.pr.out
profile	/app/data/saxs_computation/zo/5zoj/5zoj.dat

Crystal structure of human SMAD2-MAN1 complex

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

Mothers against decapentaplegic homolog 2

State in the Current Structure

Other States of the Same Protein in the Database

Inner nuclear membrane protein Man1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)