7KZ0 | pdb_00007kz0

Human MBD4 glycosylase domain bound to DNA containing substrate analog 2'-deoxy-pseudouridine

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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-glycosylase	8089628	3000905	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	Isochorismatase	e7kz0A1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Isochorismatase	ECOD (develop294)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	DNA (5'-D(CPCPAPGPCPGP(P2U)PGPCPAPGPC)-3')	-	-	-
C [auth D]	DNA (5'-D(GPCPTPGPCPGPCPGPCPTPGPG)-3')	-	-	-
A	Methyl-CpG-binding domain protein 4	DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding satellite DNA binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding satellite DNA binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity hydrolase activity, acting on glycosyl bonds hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds mismatch base pair DNA N-glycosylase activity pyrimidine-specific mismatch base pair DNA N-glycosylase activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair pyrimidine deoxyribonucleotide catabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair pyrimidine deoxyribonucleotide catabolic process deoxyribonucleotide catabolic process catabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide metabolic process pyrimidine nucleotide catabolic process base-excision repair DNA modification deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process depyrimidination nucleotide catabolic process nucleoside phosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process macromolecule modification base-excision repair, AP site formation response to lipid response to chemical response to estradiol response to oxygen-containing compound	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001739	Methyl-CpG DNA binding	Domain
A	IPR045138	Methyl-CpG binding protein MeCP2/MBD4	Family
A	IPR017352	Methyl-CpG-binding domain protein 4	Family
A	IPR011257	DNA glycosylase	Homologous Superfamily
A	IPR016177	DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O95243	primitive neuroectodermal tumor ulcerative colitis astrocytic tumor dermatomyositis juvenile dermatomyositis malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease psoriasis autism esophageal adenocarcinoma lymphoplasmacytic lymphoma medulloblastoma ovarian cancer primitive neuroectodermal tumor ulcerative colitis astrocytic tumor dermatomyositis juvenile dermatomyositis malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease psoriasis autism esophageal adenocarcinoma lymphoplasmacytic lymphoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma Sjogren syndrome Autistic Disorder glioblastoma malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.