5LUC | pdb_00005luc

Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.8 Angstrom; internal aldimine with PLP in the active site

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth T]	d5luct_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Alanine-glyoxylate aminotransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth S]	d5lucs_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Alanine-glyoxylate aminotransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth N]	d5lucn_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Alanine-glyoxylate aminotransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth M]	d5lucm_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Alanine-glyoxylate aminotransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth G]	d5lucg_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Alanine-glyoxylate aminotransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth E]	d5luce_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Alanine-glyoxylate aminotransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5lucb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Alanine-glyoxylate aminotransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5luca_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	Alanine-glyoxylate aminotransferase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth T]	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
G [auth S]	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
E [auth M]	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8044494	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 [auth T]	AGAT_like	e5lucT2	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: AGAT_like	ECOD (1.6)
H [auth T]	Aminotran_5_N	e5lucT1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
G [auth S]	AGAT_like	e5lucS1	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: AGAT_like	ECOD (1.6)
G [auth S]	Aminotran_5_N	e5lucS2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
F [auth N]	AGAT_like	e5lucN2	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: AGAT_like	ECOD (1.6)
F [auth N]	Aminotran_5_N	e5lucN1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
E [auth M]	AGAT_like	e5lucM1	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: AGAT_like	ECOD (1.6)
E [auth M]	Aminotran_5_N	e5lucM2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
D [auth G]	AGAT_like	e5lucG1	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: AGAT_like	ECOD (1.6)
D [auth G]	Aminotran_5_N	e5lucG2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
C [auth E]	AGAT_like	e5lucE2	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: AGAT_like	ECOD (1.6)
C [auth E]	Aminotran_5_N	e5lucE1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
B	AGAT_like	e5lucB2	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: AGAT_like	ECOD (1.6)
B	Aminotran_5_N	e5lucB1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
A	AGAT_like	e5lucA2	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: AGAT_like	ECOD (1.6)
A	Aminotran_5_N	e5lucA1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth T]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
H [auth T]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
G [auth S]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
G [auth S]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
F [auth N]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
F [auth N]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E [auth M]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
E [auth M]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D [auth G]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D [auth G]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C [auth E]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C [auth E]	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	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 [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	Serine--pyruvate aminotransferase	L-serine-pyruvate transaminase activity transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding alanine-glyoxylate transaminase activity L-serine-pyruvate transaminase activity transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding alanine-glyoxylate transaminase activity amino acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity	small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process glycine biosynthetic process, by transamination of glyoxylate small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process glycine biosynthetic process, by transamination of glyoxylate proteinogenic amino acid biosynthetic process small molecule metabolic process metabolic process cellular process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process catabolic process L-cysteine catabolic process sulfur amino acid metabolic process L-cysteine metabolic process organic acid catabolic process carboxylic acid catabolic process sulfur compound metabolic process amino acid catabolic process L-amino acid catabolic process L-amino acid metabolic process cysteine metabolic process sulfur compound catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process sulfur amino acid catabolic process cysteine catabolic process small molecule catabolic process oxalic acid secretion organic anion transport carboxylic acid transport secretion transport acid secretion establishment of localization organic acid transport localization oxalate transport dicarboxylic acid transport glyoxylate metabolic process monocarboxylic acid metabolic process aldehyde metabolic process alanine catabolic process L-alanine catabolic process L-alanine metabolic process alanine metabolic process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication Notch signaling pathway signal transduction L-serine metabolic process monocarboxylic acid catabolic process glyoxylate catabolic process aldehyde catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle peroxisome microbody peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle peroxisome microbody peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site	Binding Site
A, B, C [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	IPR000192	Aminotransferase class V domain	Domain
A, B, C [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	IPR024169	Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase	Family
A, B, C [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C [auth E], D [auth G], E [auth M], A, B, C [auth E], D [auth G], E [auth M], F [auth N], G [auth S], H [auth T]	Pharos: P21549	primary hyperoxaluria type 1 primary hyperoxaluria inborn errors of metabolism nephrolithiasis urolithiasis intellectual disability pancreatic ductal adenocarcinoma nephrocalcinosis peroxisomal disease primary hyperoxaluria type 2

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.