6zmn

Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site

Method: X-RAY DIFFRACTION

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

Mothers against decapentaplegic homolog 3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 4	;DNA (5'-D(PTPGPCPAPGPGPCPGPCPGPCPCPTPGPCPA)-3') ; × 4 ACETATE ION × 1 1,2-ETHANEDIOL × 1 ZINC ION × 2 TRIETHYLENE GLYCOL × 1 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMAD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–125； UniProt 10–136 Author chain B； PDBConstruct 2–125； UniProt 10–136

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	6zmn
Deposition date deposition_date	2020-07-03
Structure title title	Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site
Keywords keywords	Smad3, transcription, TGFbeta, dimerization, hinge loop, protein engineering, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6zmn__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6zmn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6zmn__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.91 Å
Rg (electron density)	26.30 Å
Total Rg	27.14 Å
Atom count	3310
Residues	303
Excluded volume	54720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6zmn__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Mothers against decapentaplegic homolog 3
Molecular weight formula_weight	14673.1 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	2670

GPAVKRLLGWKQGDEEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVETPVLP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PTPGPCPAPGPGPCPGPCPGPCPCPTPGPCPA)-3') ;
Molecular weight formula_weight	4900.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D

TGCAGGCGCGCCTGCA

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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Unit-cell length a length_a	54.502 Å
Unit-cell length b length_b	73.416 Å
Unit-cell length c length_c	111.154 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	8

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

Resolution resolution	2.333 Å
Low-resolution limit resolution_low	26.000 Å
R factor r_factor	0.2120
R_work r_work	0.2099
R_free r_free	0.2520

Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6zmn__assembly_1__model_1

6zmn__assembly_1__model_1 | I(q)

6zmn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC 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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6zmn__assembly_1__model_1

6zmn__assembly_1__model_1 | I(q)

6zmn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)