SAXSdb — 6c2f

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

Methyl-CpG-binding domain protein 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	12-mer DNA × 1 12-mer DNA × 1 UNKNOWN LIGAND × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	12-mer DNA × 1 12-mer DNA × 1 UNKNOWN LIGAND × 2	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	12-mer DNA × 1 12-mer DNA × 1 UNKNOWN LIGAND × 2	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 2	12-mer DNA × 1 12-mer DNA × 1 UNKNOWN LIGAND × 2	Consistent with all polymers
5	Protein–DNA	Monomer	Protein 1 DNA 2	12-mer DNA × 1 12-mer DNA × 1 UNKNOWN LIGAND × 2	Consistent with all polymers
6	Protein–DNA	Monomer	Protein 1 DNA 2	12-mer DNA × 1 12-mer DNA × 1 UNKNOWN LIGAND × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MBD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–79； UniProt 143–220 Author chain D； PDBConstruct 2–79； UniProt 143–220 Author chain G； PDBConstruct 2–79； UniProt 143–220 Author chain J； PDBConstruct 2–79； UniProt 143–220 Author chain M； PDBConstruct 2–79； UniProt 143–220 Author chain P； PDBConstruct 2–79； UniProt 143–220

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	6c2f
Deposition date deposition_date	2018-01-08
Structure title title	MBD2 in complex with methylated DNA
Keywords keywords	methylated dna, dna binding, 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. 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6c2f__assembly_1__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`6c2f__assembly_2__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
3	1	`6c2f__assembly_3__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
4	1	`6c2f__assembly_4__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
5	1	`6c2f__assembly_5__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
6	1	`6c2f__assembly_6__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Methyl-CpG-binding domain protein 2
Molecular weight formula_weight	8791.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J,M,P
Atom count atom_count	5915

GATESGKRMDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNTVDLSSFDFRTGKMMPSKLQK

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	12-mer DNA
Molecular weight formula_weight	3726.5 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,E,H,K,N,Q

GAGACCGGTAGC

Entity 3 Entity 3 polymer

Description description	12-mer DNA
Molecular weight formula_weight	3614.4 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,F,I,L,O,R

GCTACCGGTCTC

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	11

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6c2fA00
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

Domain ID domain_id	6c2fD00
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

Domain ID domain_id	6c2fG00
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

Domain ID domain_id	6c2fJ00
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

Domain ID domain_id	6c2fM00
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

Domain ID domain_id	6c2fP00
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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Unit-cell length a length_a	40.510 Å
Unit-cell length b length_b	40.600 Å
Unit-cell length c length_c	202.380 Å
Unit-cell angle α angle_alpha	90.07 °
Unit-cell angle β angle_beta	93.11 °
Unit-cell angle γ angle_gamma	119.75 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	35.099 Å
R factor r_factor	0.2130
R_work r_work	0.2115
R_free r_free	0.2422

MBD2 in complex with methylated DNA

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

Methyl-CpG-binding domain protein 2

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

MBD2 in complex with methylated DNA

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

Methyl-CpG-binding domain protein 2

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)