6FL5 | pdb_00006fl5

Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution

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	PLP-dependent transferases	8032405	3000954	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	PLP-dependent transferases	8032405	3000954	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	PLP-dependent transferases	8032405	3000954	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	PLP-dependent transferases	8032405	3000954	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	SHMT	e6fl5A2	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	e6fl5A1	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)
B [auth D]	SHMT	e6fl5D2	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)
B [auth D]	Aminotran_5_N	e6fl5D1	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)
C [auth G]	SHMT	e6fl5G2	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)
C [auth G]	Aminotran_5_N	e6fl5G1	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)
D [auth J]	SHMT	e6fl5J2	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)
D [auth J]	Aminotran_5_N	e6fl5J1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
B [auth D]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
C [auth G]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
D [auth J]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth D], C [auth G], D [auth J]	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, B [auth D], C [auth G], D [auth J]	Serine hydroxymethyltransferase, cytosolic	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding cation binding organic acid binding serine binding amino acid binding carboxylic acid binding translation regulator activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding cation binding organic acid binding serine binding amino acid binding carboxylic acid binding translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor 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 catalytic activity lyase activity carbon-carbon lyase activity aldehyde-lyase activity RNA binding mRNA 5'-UTR binding nucleic acid binding mRNA binding	regulation of cellular process negative regulation of biological process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation regulation of cellular process negative regulation of biological process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process pyrimidine deoxyribonucleotide biosynthetic process nucleobase-containing small molecule metabolic process dTMP metabolic process phosphate-containing compound metabolic process deoxyribonucleoside monophosphate biosynthetic process dTMP biosynthetic process small molecule metabolic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process pyrimidine-containing compound biosynthetic process nucleoside monophosphate metabolic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process nucleotide metabolic process deoxyribose phosphate metabolic process nucleobase-containing compound biosynthetic process deoxyribonucleoside monophosphate metabolic process nucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis nucleobase biosynthetic process purine nucleobase metabolic process purine nucleobase biosynthetic process purine-containing compound metabolic process purine-containing compound biosynthetic process nucleobase metabolic process folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process 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 catabolic process organic acid metabolic process L-serine catabolic process alpha-amino acid metabolic process carboxylic acid catabolic process amino acid catabolic process L-amino acid catabolic process carboxylic acid metabolic 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 glycine metabolic process carnitine metabolic process amino-acid betaine biosynthetic process carnitine biosynthetic process modified amino acid biosynthetic process amino-acid betaine metabolic process dicarboxylic acid metabolic process vitamin metabolic process amide metabolic process water-soluble vitamin metabolic process folic acid metabolic process response to peptide response to stimulus response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor organic acid biosynthetic process carboxylic acid biosynthetic process glycine biosynthetic process glycine biosynthetic process from serine small molecule biosynthetic process amino acid biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process cellular response to nitrogen compound cellular response to stimulus response to tetrahydrofolate cellular response to tetrahydrofolate response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D], C [auth G], D [auth J]	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding Site
A, B [auth D], C [auth G], D [auth J]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B [auth D], C [auth G], D [auth J]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B [auth D], C [auth G], D [auth J]	IPR039429	Serine hydroxymethyltransferase-like domain	Domain
A, B [auth D], C [auth G], D [auth J]	IPR001085	Serine hydroxymethyltransferase	Family
A, B [auth D], C [auth G], D [auth J]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B [auth D], C [auth G], D [auth J]	IPR049943	Serine hydroxymethyltransferase-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth D], C [auth G], D [auth J]	Pharos: P34896	nervous system disorder breast carcinoma Lymphoma, Small Noncleaved-Cell nephrosclerosis pancreatic ductal adenocarcinoma reticulum cell sarcoma atypical teratoid rhabdoid tumor psoriasis schizophrenia breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma lung adenocarcinoma lymphosarcoma non-Hodgkin lymphoma nervous system disorder breast carcinoma Lymphoma, Small Noncleaved-Cell nephrosclerosis pancreatic ductal adenocarcinoma reticulum cell sarcoma atypical teratoid rhabdoid tumor psoriasis schizophrenia breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma lung adenocarcinoma lymphosarcoma non-Hodgkin lymphoma attention deficit hyperactivity disorder, inattentive type esophageal adenocarcinoma large cell medulloblastoma

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.