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
- 1DGD
- Type
- protein
- Length
- 431 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dialkylglycine decarboxylase
- EC
- 4.1.1.64
- UniProt
- P16932
- Ligands
- PLP, NA, LI
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dialkylglycine decarboxylase (EC 4.1.1.64) | protein | 431 | 41% helix, 19% strand | P16932 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- NA · Sodium ion · metal · chains A
- LI · Lithium ion · metal · 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.51 | 0.76 | 26 | empty |
| 2 | 157 | 0.49 | 0.78 | 31 | PLP, MES |
| 3 | 147 | 0.41 | 0.74 | 20 | empty |
| 4 | 77 | 0.39 | 0.78 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1DGD · 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 1DGD · PDBe 1DGD · UniProt P16932
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.