4O6Z | pdb_00004o6z

Crystal structure of serine hydroxymethyltransferase with covalently bound PLP Schiff-base from Plasmodium falciparum

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)
A	d4o6za1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
A	d4o6za2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
B	d4o6zb1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
B	d4o6zb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
C	d4o6zc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
D	d4o6zd1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
D	d4o6zd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLP-dependent transferases	8073329	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8073329	3000954	SCOP2B (2022-06-29)
C	SCOP2 Family	GABA-aminotransferase-like	8073328	4000675	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	PLP-dependent transferases	8073329	3000954	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8073329	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		e4o6zA1	A: Outer membrane meander beta-barrels	X: Porins	H: Porin	T: Hormone_recep	F:	ECOD (20:10:01)
B		e4o6zB1	A: Outer membrane meander beta-barrels	X: Porins	H: Porin	T: Hormone_recep	F:	ECOD (20:10:01)
C		e4o6zC1	A: Outer membrane meander beta-barrels	X: Porins	H: Porin	T: Hormone_recep	F:	ECOD (20:10:01)
D		e4o6zD1	A: Outer membrane meander beta-barrels	X: Porins	H: Porin	T: Hormone_recep	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
B	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)
C	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)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	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	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding glycine hydroxymethyltransferase activity hydroxymethyl-, formyl- and related transferase activity	small molecule metabolic process metabolic process cellular process one-carbon metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process methylation tetrahydrofolate interconversion oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process small molecule metabolic process metabolic process cellular process one-carbon metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process methylation tetrahydrofolate interconversion oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process D-serine metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process D-amino acid metabolic 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 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid apicoplast membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid apicoplast membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

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

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.