MolNFT v1 · #27277 · protein
Crystal structure of the complex of escherichia COLI gada with glutarate at 2.05 a resolution
1XEY · Glutamate decarboxylase alpha: “Crystal structure of the complex of escherichia COLI gada with glutarate at 2.05 a resolution”. X-ray diffraction, 2 ligands (PLP, GUA), 15 pockets (best druggability 0.73). MolNFT v1 #27277 on…
- PDB
- 1XEY
- Type
- protein
- Length
- 897 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate decarboxylase alpha
- EC
- 4.1.1.15
- UniProt
- P69908
- Ligands
- PLP, GUA
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate decarboxylase alpha (EC 4.1.1.15) | protein | 448 | 42% helix, 17% strand | P69908 |
| B | Glutamate decarboxylase alpha (EC 4.1.1.15) | protein | 449 | 42% helix, 16% strand | P69908 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GUA · Glutaric acid · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.73 | 0.80 | 57 | GUA, PLP |
| 2 | 74 | 0.70 | 0.95 | 20 | empty |
| 3 | 530 | 0.69 | 0.79 | 35 | GUA |
| 4 | 209 | 0.65 | 0.84 | 36 | empty |
| 5 | 209 | 0.58 | 0.80 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 4921 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1XEY · Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 A… · the same entry in another collection · chain A against A, TM-score 1.00
- P69908 · AlphaFold monomer V2.0 prediction for glutamate decarboxylase alpha (P69908) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P69908
- Elsewhere: RCSB PDB 1XEY · PDBe 1XEY · UniProt P69908
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