3HBX | pdb_00003hbx

Crystal structure of GAD1 from Arabidopsis thaliana

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)
A	d3hbxa_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d3hbxb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d3hbxc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d3hbxd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d3hbxf_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d3hbxe_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	mouse-ear cress,thale-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)
A	SCOP2B Superfamily	PLP-dependent transferases	8083039	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8083039	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8083039	3000954	SCOP2B (2022-06-29)
D	SCOP2 Family	Pyridoxal-dependent decarboxylase	8083038	4003328	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	PLP-dependent transferases	8083039	3000954	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	PLP-dependent transferases	8083039	3000954	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLP-dependent transferases	8083039	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		e3hbxA2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)
B		e3hbxB2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)
C		e3hbxC2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)
D		e3hbxD2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)
F		e3hbxF2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)
E		e3hbxE2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
B	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
C	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
D	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
F	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
F	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
F	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)
E	4.10.280.50	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B		CATH (4.3.0)
E	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E	3.90.1150.160	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00282	Pyridoxal-dependent decarboxylase conserved domain (Pyridoxal_deC)	Pyridoxal-dependent decarboxylase conserved domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Glutamate decarboxylase 1	protein binding binding calmodulin binding molecular adaptor activity glutamate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding protein binding binding calmodulin binding molecular adaptor activity glutamate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding	catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process L-glutamate catabolic process dicarboxylic acid metabolic process L-amino acid catabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process L-glutamate catabolic process dicarboxylic acid metabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR010107	Glutamate decarboxylase	Family
A, B, C, D, E A, B, C, D, E, F	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002129	Pyridoxal phosphate-dependent decarboxylase, major domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F	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.