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The X-ray crystal structure of the 67KDA isoform of glutamic acid decarboxylase (GAD67)
Analyse The X-ray crystal structure of the 67KDA isoform of glutamic acid decarboxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OKJ
- Type
- protein
- Length
- 1,005 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate decarboxylase 1
- EC
- 4.1.1.15
- UniProt
- Q99259
- Ligands
- ABU, PLZ
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate decarboxylase 1 (EC 4.1.1.15) | protein | 501 | 46% helix, 14% strand | Q99259 |
| B | Glutamate decarboxylase 1 (EC 4.1.1.15) | protein | 504 | 45% helix, 13% strand | Q99259 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 2 copies · chains A, B
- PLZ · 4-[({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methyl)amino]butanoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.75 | 0.97 | 35 | ABU |
| 2 | 70 | 0.73 | 0.98 | 22 | ABU |
| 3 | 155 | 0.56 | 0.81 | 30 | empty |
| 4 | 122 | 0.53 | 0.82 | 19 | empty |
| 5 | 145 | 0.53 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 6975 Ų buried · 81 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (cofactor, covalent ligand).
Compared structures
- 2OKJ · The X-ray crystal structure of the 67kDa isoform of Glutamic Acid Decarboxylase (GAD67) · the same entry in another collection · chain A against A, TM-score 1.00
- Q99259 · AlphaFold monomer V2.0 prediction for glutamate decarboxylase 1 (Q99259) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q99259
- Elsewhere: RCSB PDB 2OKJ · PDBe 2OKJ · UniProt Q99259
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