4DA1 | pdb_00004da1

Crystal structure of branched-chain alpha-ketoacid dehydrogenase phosphatase with Mg (II) ions at the active site

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	PP2C-like	8083898	3000909	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	PARP	e4da1A1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PARP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.40.10	Alpha Beta	4-Layer Sandwich	Phosphatase 2c	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00481	Protein phosphatase 2C (PP2C)	Protein phosphatase 2C	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein phosphatase 1K, mitochondrial	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity [3-methyl-2-oxobutanoate dehydrogenase (lipoamide)]-phosphatase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity [3-methyl-2-oxobutanoate dehydrogenase (lipoamide)]-phosphatase activity catalytic activity protein serine/threonine phosphatase activity	catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process amino acid catabolic process apoptotic mitochondrial changes biological regulation cell death cellular component organization organelle organization regulation of membrane permeability regulation of mitochondrial membrane permeability involved in apoptotic process apoptotic process cellular component organization or biogenesis regulation of biological quality regulation of mitochondrial membrane permeability programmed cell death mitochondrion organization cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process response to stimulus signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication signal transduction	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036457	PPM-type phosphatase-like domain superfamily	Homologous Superfamily
A	IPR015655	Protein phosphatase 2C	Family
A	IPR000222	PPM-type phosphatase, divalent cation binding	Binding Site
A	IPR001932	PPM-type phosphatase-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8N3J5	maple syrup urine disease maple syrup urine disease, mild variant pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor Crohn disease intermediate maple syrup urine disease large cell medulloblastoma malignant glioma Maple Syrup Urine Disease, Thiamine Responsive osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis breast cancer glioblastoma maple syrup urine disease maple syrup urine disease, mild variant pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor Crohn disease intermediate maple syrup urine disease large cell medulloblastoma malignant glioma Maple Syrup Urine Disease, Thiamine Responsive osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis breast cancer glioblastoma intermittent maple syrup urine disease lung adenocarcinoma medulloblastoma ovarian cancer pituitary cancer classic maple syrup urine disease gout juvenile dermatomyositis malignant ependymoma oligodendroglioma

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.