6CNP | pdb_00006cnp

Crystal structure of MBD2 complex with methylated CpG island

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	SCOP2B Superfamily	DNA-binding domain	8081855	3000183	SCOP2B (2022-06-29)
A	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)
B		e6cnpB1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: F_bP_aldolase	F:	ECOD (20:10:01)
A		e6cnpA1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: F_bP_aldolase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D, E, F	DNA (5'-D(GPCPCPAPCP(5CM)PGPGPTPGPGPC)-3')	-	-	-
A, B	Methyl-CpG-binding domain protein 2	protein binding binding protein domain specific binding regulatory RNA binding RNA binding siRNA binding nucleic acid binding chromatin binding C2H2 zinc finger domain binding mRNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding protein binding binding protein domain specific binding regulatory RNA binding RNA binding siRNA binding nucleic acid binding chromatin binding C2H2 zinc finger domain binding mRNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding satellite DNA binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding molecular adaptor activity identical protein binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular 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 component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis response to stimulus response to chemical response to oxygen-containing compound response to bisphenol A maternal behavior behavior multicellular organismal process parental behavior reproductive process multicellular organismal reproductive process reproductive behavior developmental process heart development cardiac muscle tissue development animal organ development tissue development striated muscle tissue development circulatory system development multicellular organism development ventricular cardiac muscle tissue development anatomical structure development muscle tissue development system development embryonic organ development embryo development chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic cellular response to nitrogen compound cellular response to stimulus response to serotonin cellular response to serotonin response to monoamine response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to monoamine stimulus response to mechanical stimulus response to abiotic stimulus response to external stimulus positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cell population proliferation regulation of cell population proliferation response to nutrient levels transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II response to lipid response to estradiol	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex ATPase complex nuclear protein-containing complex transcription regulator complex histone deacetylase complex NuRD complex SWI/SNF superfamily-type complex catalytic complex CHD-type complex heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.