MolNFT v1 · #82504 · protein
Structural characterization of glutamic acid decarboxylase; insights into the mechanism of autoinactivation
3VP6 · Glutamate decarboxylase 1: “Structural characterization of glutamic acid decarboxylase; insights into the mechanism of autoinactivation”. X-ray diffraction, 1 ligand (HLD), 11 pockets (best druggability 0.82). MolNFT v1 #82504 on…
- PDB
- 3VP6
- Type
- protein
- Length
- 991 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
- HLD
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate decarboxylase 1 (EC 4.1.1.15) | protein | 500 | 47% helix, 14% strand | Q99259 |
| B | Glutamate decarboxylase 1 (EC 4.1.1.15) | protein | 491 | 46% helix, 14% strand | Q99259 |
Ligands and binding sites
- HLD · 4-oxo-4H-pyran-2,6-dicarboxylic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.82 | 0.97 | 45 | HLD |
| 2 | 860 | 0.77 | 0.80 | 63 | HLD |
| 3 | 57 | 0.67 | 0.95 | 18 | empty |
| 4 | 77 | 0.64 | 0.91 | 22 | empty |
| 5 | 165 | 0.56 | 0.81 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 6647 Ų buried · 75 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 3VP6 · Structural characterization of Glutamic Acid Decarboxylase; insights into the mechanism… · 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 3VP6 · PDBe 3VP6 · UniProt Q99259
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