SAXSdb — 6d1t

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

Methyl-CpG-binding domain protein 1

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–77	Fragment：residues 1-77	;DNA (5'-D(GPCPCPAPAP(5CM)PGPTPTPGPGPC)-3') ; × 2 UNX UNKNOWN LIGAND × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；30% PEG-550-MME, 0.1 M magnesium chloride, 0.1 M HEPES	Resolution 2.25 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 6D1T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D9N SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1/PCM1 Deposited 1999-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–75（75 aa） Fragment：METHYL-CPG-BINDING DOMAIN OF MBD1	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 50mM KCL；Pressure 1 NMR sample composition 1.3MM MBD U-15N,13C; 20MM PHOSPHATE BUFFER; 50MM KCL; 5MM DTT	Resolution not provided
1IG4 Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA Deposited 2001-04-17	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–75（75 aa） Fragment：Methyl-CpG-binding domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K NMR sample composition 1.3mM MBD1(U-15N,13C)-DNA Complex; 20mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 1.3mM MBD1(U-15N,13C)-DNA Complex; 20mM phosphate buffer \| 100% D2O NMR sample composition 1mM MBD1(U-15N)-DNA Complex; 20mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
4D4W Solution structure of human MBD1 CXXC1 domain Deposited 2014-10-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 167–222（56 aa） Fragment：RESIDUES 167-222	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 0.25；Pressure 1.0 NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 0.25；Pressure 1.0 NMR sample composition 95% H2O/5% D2O	Resolution not provided
5W9Q Zinc finger region of MBD1 in complex with CpG DNA Deposited 2017-06-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 330–388（59 aa） Fragment：Zinc finger region (UNP residues 330-388)	Not recorded	ZN ZINC ION × 2 UNX UNKNOWN LIGAND × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG-400, 0.2 M magnesium chloride, 0.1 M hepes	Resolution 1.80 Å R-free 0.253
5W9Q Zinc finger region of MBD1 in complex with CpG DNA Deposited 2017-06-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 330–388（59 aa） Fragment：Zinc finger region (UNP residues 330-388)	Not recorded	ZN ZINC ION × 2 UNX UNKNOWN LIGAND × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG-400, 0.2 M magnesium chloride, 0.1 M hepes	Resolution 1.80 Å R-free 0.253

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

View Construct and Data Evidence

UniProt name	MBD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–79； UniProt 1–77

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	6d1t
Deposition date deposition_date	2018-04-12
Structure title title	Complex of MBD1-MBD and methylated DNA
Keywords keywords	mbd, dna-methylation, Structural Genomics, Structural Genomics Consortium, SGC, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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

该条目暂无 SAXS 数据。

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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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	Methyl-CpG-binding domain protein 1
Molecular weight formula_weight	8870.1 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	1038

GSMAEDWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLTLFDFKQGILCYPAPKAH

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 2 Entity 2 polymer

Description description	;DNA (5'-D(GPCPCPAPAP(5CM)PGPTPTPGPGPC)-3') ;
Molecular weight formula_weight	3677.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C

GCCAACGTTGGC

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	12

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6d1tA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	890 — Methyl-cpg-binding Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Methyl-cpg-binding Protein 2; Chain A

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8. Citations (1)

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Unit-cell length a length_a	28.574 Å
Unit-cell length b length_b	74.193 Å
Unit-cell length c length_c	138.872 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	37.100 Å
R factor r_factor	0.2382
R_work r_work	0.2349
R_free r_free	0.2693

Complex of MBD1-MBD and methylated DNA

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

Methyl-CpG-binding domain protein 1

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (0)