6CZZ | pdb_00006czz

Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP-phosphoserine geminal diamine intermediate

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	d6czzd1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d6czzd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d6czzc1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d6czzc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d6czzb1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d6czzb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d6czza1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d6czza2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	8078934	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8078934	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8078934	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8078934	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	DEAD	e6czzD2	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
D	Lactamase_B	e6czzD3	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Lactamase_B	ECOD (develop294)
C	DEAD	e6czzC2	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
C	Lactamase_B	e6czzC3	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Lactamase_B	ECOD (develop294)
B	DEAD	e6czzB1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
B	Lactamase_B	e6czzB2	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Lactamase_B	ECOD (develop294)
A	DEAD	e6czzA1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
A	Lactamase_B	e6czzA2	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Lactamase_B	ECOD (develop294)

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	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, C, D	Phosphoserine aminotransferase 1, chloroplastic	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 nitrogenous groups transaminase 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 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle plastid stroma chloroplast stroma chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site	Binding Site
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	IPR022278	Phosphoserine aminotransferase	Family
A, B, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR000192	Aminotransferase class V domain	Domain

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.