1DFO | pdb_00001dfo

CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1dfod_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1dfoc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1dfob_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1dfoa_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	Serine hydroxymethyltransferase	(Escherichia coli ) [TaxId: 562 ],	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	8032404	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8032404	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8032404	3000954	SCOP2B (2022-06-29)
A	SCOP2 Family	GABA-aminotransferase-like	8020024	4000675	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8032404	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)
D	Aminotran_3	e1dfoD2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Aminotran_3	ECOD (v294.1)
D	Phosphodiest, Metalloenzyme	e1dfoD3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)
C	Aminotran_3	e1dfoC2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Aminotran_3	ECOD (v294.1)
C	Phosphodiest, Metalloenzyme	e1dfoC3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)
B	Aminotran_3	e1dfoB2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Aminotran_3	ECOD (v294.1)
B	Phosphodiest, Metalloenzyme	e1dfoB3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)
A	Aminotran_3	e1dfoA2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Aminotran_3	ECOD (v294.1)
A	Phosphodiest, Metalloenzyme	e1dfoA3	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, C, D	SERINE HYDROXYMETHYLTRANSFERASE	threonine aldolase activity L-allo-threonine aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding threonine aldolase activity L-allo-threonine aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity cation binding transition metal ion binding zinc ion binding metal ion binding	folic acid-containing compound metabolic process modified amino acid metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process tetrahydrofolate interconversion small molecule metabolic process one-carbon metabolic process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process tetrahydrofolate interconversion small molecule metabolic process one-carbon metabolic process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process L-serine catabolic process alpha-amino acid metabolic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process small molecule catabolic process amino acid catabolic process organic acid biosynthetic process glycine biosynthetic process from L-serine carboxylic acid biosynthetic process glycine metabolic 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 L-amino acid biosynthetic process L-serine biosynthetic process glycine catabolic process	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

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.