8A5W | pdb_00008a5w

Crystal structure of the human phosphoserine aminotransferase (PSAT) in complex with O-phosphoserine

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	PLP-dependent transferases	8078936	3000954	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PLP-dependent transferases	8078936	3000954	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	PLP-dependent transferases	8078936	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8078936	3000954	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	PLP-dependent transferases	8078936	3000954	SCOP2B (2022-06-29)
F [auth A]	SCOP2B Superfamily	PLP-dependent transferases	8078936	3000954	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	PLP-dependent transferases	8078936	3000954	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	PLP-dependent transferases	8078936	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	F_UNCLASSIFIED	e8a5wH2	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: F_UNCLASSIFIED	ECOD (1.6)
H	F_UNCLASSIFIED	e8a5wH1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e8a5wG2	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: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e8a5wG1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth B]	F_UNCLASSIFIED	e8a5wB2	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: F_UNCLASSIFIED	ECOD (1.6)
D [auth B]	F_UNCLASSIFIED	e8a5wB1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8a5wC2	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: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8a5wC1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth E]	F_UNCLASSIFIED	e8a5wE2	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: F_UNCLASSIFIED	ECOD (1.6)
B [auth E]	F_UNCLASSIFIED	e8a5wE1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth A]	F_UNCLASSIFIED	e8a5wA1	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: F_UNCLASSIFIED	ECOD (1.6)
F [auth A]	F_UNCLASSIFIED	e8a5wA2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth F]	F_UNCLASSIFIED	e8a5wF2	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: F_UNCLASSIFIED	ECOD (1.6)
E [auth F]	F_UNCLASSIFIED	e8a5wF1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)
A [auth D]	F_UNCLASSIFIED	e8a5wD1	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: F_UNCLASSIFIED	ECOD (1.6)
A [auth D]	F_UNCLASSIFIED	e8a5wD2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E], C, D [auth B], 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
A [auth D], E [auth F], F [auth A]	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
B [auth E], C, D [auth B], G, H	Phosphoserine aminotransferase	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 identical protein binding 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 identical protein binding protein binding	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process oxoacid metabolic 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 proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol
A [auth D], E [auth F], F [auth A]	Phosphoserine aminotransferase	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 identical protein binding 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 identical protein binding protein binding	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process oxoacid metabolic 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 proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth E], C, D [auth B], G, H	Pharos: Q9Y617	PSAT deficiency non-small cell lung carcinoma Neu-Laxova syndrome 2 Neu-Laxova syndrome Neu-Laxova syndrome 1 lung adenocarcinoma malignant ependymoma medulloblastoma Adenocarcinoma of Lung ovarian cancer atypical teratoid rhabdoid tumor pilocytic astrocytoma psoriasis exocrine pancreatic carcinoma ulcerative colitis PSAT deficiency non-small cell lung carcinoma Neu-Laxova syndrome 2 Neu-Laxova syndrome Neu-Laxova syndrome 1 lung adenocarcinoma malignant ependymoma medulloblastoma Adenocarcinoma of Lung ovarian cancer atypical teratoid rhabdoid tumor pilocytic astrocytoma psoriasis exocrine pancreatic carcinoma ulcerative colitis hepatocellular carcinoma leukodystrophy lung carcinoma malignant mesothelioma myelodysplastic syndrome oligodendroglioma adrenoleukodystrophy pancreatic ductal adenocarcinoma Crohn disease polycystic ovary syndrome Down syndrome schizophrenia gastric cancer intellectual disability malignant colon neoplasm malignant pancreatic neoplasm nasopharyngeal carcinoma osteosarcoma attention deficit hyperactivity disorder, inattentive type pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cystic fibrosis subependymal giant cell astrocytoma gastric carcinoma large cell medulloblastoma lung cancer
A [auth D], E [auth F], F [auth A]	Pharos: Q9Y617	PSAT deficiency non-small cell lung carcinoma Neu-Laxova syndrome 2 Neu-Laxova syndrome Neu-Laxova syndrome 1 lung adenocarcinoma malignant ependymoma medulloblastoma Adenocarcinoma of Lung ovarian cancer atypical teratoid rhabdoid tumor pilocytic astrocytoma psoriasis exocrine pancreatic carcinoma ulcerative colitis PSAT deficiency non-small cell lung carcinoma Neu-Laxova syndrome 2 Neu-Laxova syndrome Neu-Laxova syndrome 1 lung adenocarcinoma malignant ependymoma medulloblastoma Adenocarcinoma of Lung ovarian cancer atypical teratoid rhabdoid tumor pilocytic astrocytoma psoriasis exocrine pancreatic carcinoma ulcerative colitis hepatocellular carcinoma leukodystrophy lung carcinoma malignant mesothelioma myelodysplastic syndrome oligodendroglioma adrenoleukodystrophy pancreatic ductal adenocarcinoma Crohn disease polycystic ovary syndrome Down syndrome schizophrenia gastric cancer intellectual disability malignant colon neoplasm malignant pancreatic neoplasm nasopharyngeal carcinoma osteosarcoma attention deficit hyperactivity disorder, inattentive type pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cystic fibrosis subependymal giant cell astrocytoma gastric carcinoma large cell medulloblastoma lung cancer

Protein Modification Annotation

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