6DK3

HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASe 2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6dk3a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GABA-aminotransferase-like	8024349	4000675	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8036728	3000954	SCOP2 (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	SHMT	e6dk3A1	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
A	Aminotran_5_N	e6dk3A2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00464	Serine hydroxymethyltransferase (SHMT)	Serine hydroxymethyltransferase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Serine hydroxymethyltransferase, mitochondrial	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding cation binding organic acid binding serine binding amino acid binding carboxylic acid binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding cation binding organic acid binding serine binding amino acid binding carboxylic acid binding protein-containing complex binding chromatin binding translation regulator activity mRNA regulatory element binding translation repressor activity translation regulator activity, nucleic acid binding nucleic acid binding translation repressor activity threonine aldolase activity L-allo-threonine aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity RNA binding mRNA 5'-UTR binding mRNA binding transition metal ion binding zinc ion binding metal ion binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein homotetramerization protein homooligomerization organonitrogen compound metabolic process nucleobase biosynthetic process purine nucleobase metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein homotetramerization protein homooligomerization organonitrogen compound metabolic process nucleobase biosynthetic process purine nucleobase metabolic process organonitrogen compound biosynthetic process purine nucleobase biosynthetic process primary metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process small molecule metabolic process metabolic process cellular metabolic process cellular modified amino acid metabolic process folic acid-containing compound metabolic process tetrahydrofolate interconversion tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process catabolic process serine family amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process L-serine catabolic process alpha-amino acid metabolic process cellular catabolic process carboxylic acid catabolic process amino acid catabolic process organonitrogen compound catabolic process carboxylic acid metabolic process L-amino acid catabolic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process serine family amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process organic substance catabolic process protein deubiquitination protein K63-linked deubiquitination protein modification by small protein removal macromolecule modification protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal cellular biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process L-serine biosynthetic process amino acid biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process mitochondrial translation regulation of mitochondrial gene expression mitochondrial gene expression regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of biosynthetic process regulation of protein metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression regulation of mitochondrial translation regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process response to organic substance biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response response to cytokine defense response to symbiont response to external stimulus response to biotic stimulus response to chemical immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus response to type I interferon aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration regulation of oxidative phosphorylation glycine metabolic process dicarboxylic acid metabolic process vitamin metabolic process amide metabolic process water-soluble vitamin metabolic process folic acid metabolic process glycine biosynthetic process glycine biosynthetic process from serine	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle protein-containing complex BRISC complex nucleus nuclear protein-containing complex membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial nucleoid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding Site
A	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A	IPR039429	Serine hydroxymethyltransferase-like domain	Domain
A	IPR001085	Serine hydroxymethyltransferase	Family
A	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P34897	non-small cell lung carcinoma nasopharyngeal carcinoma osteosarcoma plasma cell myeloma Sjogren syndrome abdominal aortic aneurysm astrocytic tumor breast cancer colorectal cancer heart disease lung cancer malignant glioma ovarian cancer Plasmodium vivax malaria acute myeloid leukemia non-small cell lung carcinoma nasopharyngeal carcinoma osteosarcoma plasma cell myeloma Sjogren syndrome abdominal aortic aneurysm astrocytic tumor breast cancer colorectal cancer heart disease lung cancer malignant glioma ovarian cancer Plasmodium vivax malaria acute myeloid leukemia atopic eczema cardiomyopathy diabetes mellitus large cell medulloblastoma malignant colon neoplasm medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma psoriasis adrenal cortex carcinoma autism spectrum disorder colorectal adenoma glioblastoma lung adenocarcinoma malignant ependymoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.