Research workbench
An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase
Analyse An alkali metal ion size-dependent switch in the active site structure of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DGE
- Type
- protein
- Length
- 431 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Burkholderia cepacia
- Molecule
- Dialkylglycine decarboxylase
- EC
- 4.1.1.64
- UniProt
- P16932
- Ligands
- PLP, RB
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · resolution 2.8 · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dialkylglycine decarboxylase (EC 4.1.1.64) | protein | 431 | 40% helix, 19% strand | P16932 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- RB · Rubidium ion · metal · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.51 | 0.76 | 44 | PLP, MES |
| 2 | 202 | 0.49 | 0.75 | 27 | empty |
| 3 | 176 | 0.45 | 0.74 | 23 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1DGE · An alkali metal ion size-dependent switch in the active site structure of dialkylglycine… · the same entry in another collection · chain A against A, TM-score 1.00
- P16932 · AlphaFold monomer V2.0 prediction for 2,2-dialkylglycine decarboxylase (P16932) · 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 P16932
- Elsewhere: RCSB PDB 1DGE · PDBe 1DGE · UniProt P16932
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