3ECD | pdb_00003ecd

Crystal structure of serine hydroxymethyltransferase from Burkholderia pseudomallei

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d3ecdd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
C	d3ecdc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
B	d3ecdb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
A	d3ecda_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	GABA-aminotransferase-like	8075105	4000675	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	PLP-dependent transferases	8075106	3000954	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8075106	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8075106	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8075106	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	RB_A	e3ecdD1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: RB_A	ECOD (v294.1)
D	Phosphodiest, Metalloenzyme	e3ecdD2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)
C	RB_A	e3ecdC1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: RB_A	ECOD (v294.1)
C	Phosphodiest, Metalloenzyme	e3ecdC2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)
B	RB_A	e3ecdB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: RB_A	ECOD (v294.1)
B	Phosphodiest, Metalloenzyme	e3ecdB2	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.1)
A	RB_A	e3ecdA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: RB_A	ECOD (v294.1)
A	Phosphodiest, Metalloenzyme	e3ecdA2	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Serine hydroxymethyltransferase 2	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding 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 catalytic activity	folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process metabolic process cellular process small molecule metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process glycine biosynthetic process from L-serine folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process metabolic process cellular process small molecule metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process glycine biosynthetic process from L-serine alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
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	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.