5F8V | pdb_00005f8v

Crystal structure of PLP bound phosphoserine aminotransferase (PSAT) from Trichomonas vaginalis

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d5f8vh_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
G	d5f8vg_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
F	d5f8vf_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
E [auth D]	d5f8vd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
D [auth C]	d5f8vc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
C [auth B]	d5f8vb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
B [auth E]	d5f8ve_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)
A	d5f8va_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Trichomonas vaginalis ) [TaxId: 5722 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	PLP-dependent transferases	8078938	3000954	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PLP-dependent transferases	8078938	3000954	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PLP-dependent transferases	8078938	3000954	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	PLP-dependent transferases	8078938	3000954	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	PLP-dependent transferases	8078938	3000954	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	PLP-dependent transferases	8078938	3000954	SCOP2B (2022-06-29)
B [auth E]	SCOP2 Family	GABA-aminotransferase-like	8078937	4000675	SCOP2 (2022-06-29)
B [auth E]	SCOP2 Superfamily	PLP-dependent transferases	8078938	3000954	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8078938	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)
H	Aminotran_5_C_1	e5f8vH2	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: Aminotran_5_C_1	ECOD (1.6)
H	UNK_F_TYPE	e5f8vH3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: UNK_F_TYPE	ECOD (1.6)
G	Aminotran_5_C_1	e5f8vG2	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: Aminotran_5_C_1	ECOD (1.6)
G	UNK_F_TYPE	e5f8vG3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: UNK_F_TYPE	ECOD (1.6)
F	Aminotran_5_C_1	e5f8vF2	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: Aminotran_5_C_1	ECOD (1.6)
F	UNK_F_TYPE	e5f8vF3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: UNK_F_TYPE	ECOD (1.6)
E [auth D]	Aminotran_5_C_1	e5f8vD1	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: Aminotran_5_C_1	ECOD (1.6)
E [auth D]	UNK_F_TYPE	e5f8vD2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: UNK_F_TYPE	ECOD (1.6)
D [auth C]	Aminotran_5_C_1	e5f8vC2	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: Aminotran_5_C_1	ECOD (1.6)
D [auth C]	UNK_F_TYPE	e5f8vC3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: UNK_F_TYPE	ECOD (1.6)
C [auth B]	Aminotran_5_C_1	e5f8vB2	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: Aminotran_5_C_1	ECOD (1.6)
C [auth B]	UNK_F_TYPE	e5f8vB3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: UNK_F_TYPE	ECOD (1.6)
B [auth E]	Aminotran_5_C_1	e5f8vE2	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: Aminotran_5_C_1	ECOD (1.6)
B [auth E]	UNK_F_TYPE	e5f8vE3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: UNK_F_TYPE	ECOD (1.6)
A	Aminotran_5_C_1	e5f8vA2	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: Aminotran_5_C_1	ECOD (1.6)
A	UNK_F_TYPE	e5f8vA3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.2.0)
H	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.2.0)
G	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.2.0)
G	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.2.0)
F	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.2.0)
F	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.2.0)
E [auth D]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.2.0)
E [auth D]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.2.0)
D [auth C]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.2.0)
D [auth C]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.2.0)
C [auth B]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.2.0)
C [auth B]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.2.0)
B [auth E]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.2.0)
B [auth E]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.2.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.2.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	PF00266	Aminotransferase class-V (Aminotran_5)	Aminotransferase class-V	This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	Aminotransferase, class V family protein	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity O-phospho-L-serine:2-oxoglutarate aminotransferase activity	oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-serine metabolic process L-serine biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-serine metabolic process L-serine biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule metabolic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site	Binding Site
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	IPR000192	Aminotransferase class V domain	Domain
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	IPR022278	Phosphoserine aminotransferase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B [auth E], C [auth B], D [auth C], E [auth D], A, B [auth E], C [auth B], D [auth C], E [auth D], F, G, H	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.