6C2F

MBD2 in complex with methylated DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DNA-binding domain	8081855	3000183	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA-binding domain	8081855	3000183	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA-binding domain	8081855	3000183	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	DNA-binding domain	8081855	3000183	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	DNA-binding domain	8081855	3000183	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	DNA-binding domain	8081855	3000183	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF01429	e6c2fA1	A: a+b two layers	X: DNA-binding domain	H: Methyl-CpG-binding domain, MBD (From Topology)	T: Methyl-CpG-binding domain, MBD	F: PF01429	ECOD (1.6)
D	PF01429	e6c2fD1	A: a+b two layers	X: DNA-binding domain	H: Methyl-CpG-binding domain, MBD (From Topology)	T: Methyl-CpG-binding domain, MBD	F: PF01429	ECOD (1.6)
G	PF01429	e6c2fG1	A: a+b two layers	X: DNA-binding domain	H: Methyl-CpG-binding domain, MBD (From Topology)	T: Methyl-CpG-binding domain, MBD	F: PF01429	ECOD (1.6)
J	PF01429	e6c2fJ1	A: a+b two layers	X: DNA-binding domain	H: Methyl-CpG-binding domain, MBD (From Topology)	T: Methyl-CpG-binding domain, MBD	F: PF01429	ECOD (1.6)
M	PF01429	e6c2fM1	A: a+b two layers	X: DNA-binding domain	H: Methyl-CpG-binding domain, MBD (From Topology)	T: Methyl-CpG-binding domain, MBD	F: PF01429	ECOD (1.6)
P	PF01429	e6c2fP1	A: a+b two layers	X: DNA-binding domain	H: Methyl-CpG-binding domain, MBD (From Topology)	T: Methyl-CpG-binding domain, MBD	F: PF01429	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.890.10	Alpha Beta	2-Layer Sandwich	Methyl-cpg-binding Protein 2	Chain A	CATH (4.3.0)
D	3.30.890.10	Alpha Beta	2-Layer Sandwich	Methyl-cpg-binding Protein 2	Chain A	CATH (4.3.0)
G	3.30.890.10	Alpha Beta	2-Layer Sandwich	Methyl-cpg-binding Protein 2	Chain A	CATH (4.3.0)
J	3.30.890.10	Alpha Beta	2-Layer Sandwich	Methyl-cpg-binding Protein 2	Chain A	CATH (4.3.0)
M	3.30.890.10	Alpha Beta	2-Layer Sandwich	Methyl-cpg-binding Protein 2	Chain A	CATH (4.3.0)
P	3.30.890.10	Alpha Beta	2-Layer Sandwich	Methyl-cpg-binding Protein 2	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J, M A, D, G, J, M, P	PF01429	Methyl-CpG binding domain (MBD)	Methyl-CpG binding domain	The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs [1]. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-s ...	The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs [1]. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair [1]. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J, M A, D, G, J, M, P	Methyl-CpG-binding domain protein 2	protein binding binding protein domain specific binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding organic cyclic compound binding satellite DNA binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding protein binding binding protein domain specific binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding organic cyclic compound binding satellite DNA binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding molecular adaptor activity C2H2 zinc finger domain binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II protein-DNA complex organization cellular component organization chromatin organization DNA methylation-dependent heterochromatin formation chromatin remodeling cellular component organization or biogenesis heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of gene expression facultative heterochromatin formation negative regulation of gene expression, epigenetic	membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm NuRD complex membrane-bounded organelle protein-containing complex ATPase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm NuRD complex SWI/SNF superfamily-type complex non-membrane-bounded organelle catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity organelle lumen organelle intracellular non-membrane-bounded organelle CHD-type complex nuclear lumen cytoplasm cytosol
B, E, H, K, N B, E, H, K, N, Q	12-mer DNA	-	-	-
C, F, I, L, O C, F, I, L, O, R	12-mer DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J, M A, D, G, J, M, P	IPR025884	Methyl-CpG binding protein 2/3, C-terminal domain	Domain
A, D, G, J, M A, D, G, J, M, P	IPR001739	Methyl-CpG DNA binding	Domain
A, D, G, J, M A, D, G, J, M, P	IPR032343	Methyl-CpG-binding domain protein 2/3, p55-binding region	Domain
A, D, G, J, M A, D, G, J, M, P	IPR016177	DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D, G, J, M A, D, G, J, M, P	Pharos: Q9UBB5	prostate cancer atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma pilocytic astrocytoma Prostate cancer, familial schizophrenia glioblastoma lung cancer medulloblastoma primitive neuroectodermal tumor spina bifida juvenile dermatomyositis malignant ependymoma ovarian cancer prostate cancer atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma pilocytic astrocytoma Prostate cancer, familial schizophrenia glioblastoma lung cancer medulloblastoma primitive neuroectodermal tumor spina bifida juvenile dermatomyositis malignant ependymoma ovarian cancer psoriasis subependymal giant cell astrocytoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.