2OKK | pdb_00002okk

The X-ray crystal structure of the 65kDa isoform of Glutamic Acid Decarboxylase (GAD65)

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)
A	SCOP2 Family	Pyridoxal-dependent decarboxylase	8101596	4003328	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8101597	3000954	SCOP2 (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	Aminotran_3	e2okkA2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Aminotran_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1150.170	Alpha Beta	Alpha-Beta Complex	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	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	Glutamate decarboxylase 2	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding glutamate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	gamma-aminobutyric acid metabolic process 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 carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process gamma-aminobutyric acid biosynthetic process small molecule metabolic process gamma-aminobutyric acid metabolic process 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 carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process gamma-aminobutyric acid biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process non-proteinogenic amino acid biosynthetic process trans-synaptic signaling synaptic signaling regulation of biological process signaling anterograde trans-synaptic signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication catabolic process organic acid catabolic process dicarboxylic acid catabolic process alpha-amino acid metabolic process succinate metabolic process carboxylic acid catabolic process gamma-aminobutyrate shunt glutamate metabolic process amino acid catabolic process L-glutamate catabolic process dicarboxylic acid metabolic process L-amino acid catabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process	membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane cytosol membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane cytosol cell periphery plasma membrane presynapse synapse cell junction presynaptic membrane plasma membrane region synaptic membrane axon cell projection neuron projection plasma membrane bounded cell projection clathrin-sculpted gamma-aminobutyric acid transport vesicle clathrin-sculpted vesicle intracellular vesicle clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane coated vesicle membrane cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane clathrin-coated vesicle coated vesicle vesicle clathrin-coated vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A	IPR002129	Pyridoxal phosphate-dependent decarboxylase, major domain	Domain
A	IPR021115	Pyridoxal-phosphate binding site	Binding Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q05329	diabetic retinopathy cocaine dependence bipolar disorder visual epilepsy major depressive disorder cocaine abuse schizophrenia Generalized seizures inborn carbohydrate metabolic disorder malignant ependymoma astrocytic tumor autoimmune disease pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor glioblastoma diabetic retinopathy cocaine dependence bipolar disorder visual epilepsy major depressive disorder cocaine abuse schizophrenia Generalized seizures inborn carbohydrate metabolic disorder malignant ependymoma astrocytic tumor autoimmune disease pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor glioblastoma large cell medulloblastoma malignant glioma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia anxiety disorder atypical teratoid rhabdoid tumor ovarian cancer pilocytic astrocytoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	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.