6SMN | pdb_00006smn

A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with methotrexate

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6smnd1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d6smnd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d6smnc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d6smnb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d6smna_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PLP-dependent transferases	8100378	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8100378	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8100378	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8100378	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)
D	PSI_PsaE	e6smnD1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: PSI_PsaE	ECOD (develop294)
C	PSI_PsaE	e6smnC1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: PSI_PsaE	ECOD (develop294)
B	PSI_PsaE	e6smnB1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: PSI_PsaE	ECOD (develop294)
A	PSI_PsaE	e6smnA1	A: alpha bundles	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: PSI_PsaE	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF00464	Serine hydroxymethyltransferase (SHMT)	Serine hydroxymethyltransferase		Domain
A, B, C	PF00464	Serine hydroxymethyltransferase (SHMT)	Serine hydroxymethyltransferase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Serine hydroxymethyltransferase 2, mitochondrial	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity catalytic activity zinc ion binding	oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process tetrahydrofolate interconversion one-carbon metabolic process L-serine metabolic process L-amino acid metabolic process organic acid biosynthetic process glycine biosynthetic process from L-serine carboxylic acid biosynthetic process glycine biosynthetic process small molecule biosynthetic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid respiratory chain complex protein-containing complex catalytic complex membrane membrane protein complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid respiratory chain complex protein-containing complex catalytic complex membrane membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex
A, B, C	Serine hydroxymethyltransferase 2, mitochondrial	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity catalytic activity zinc ion binding	oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process tetrahydrofolate interconversion one-carbon metabolic process L-serine metabolic process L-amino acid metabolic process organic acid biosynthetic process glycine biosynthetic process from L-serine carboxylic acid biosynthetic process glycine biosynthetic process small molecule biosynthetic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid respiratory chain complex protein-containing complex catalytic complex membrane membrane protein complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid respiratory chain complex protein-containing complex catalytic complex membrane membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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.

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