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Crystal structure of dialkylglycine decarboxylases bound with calcium ion
Analyse Crystal structure of dialkylglycine decarboxylases bound with calcium ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZOB
- Type
- protein
- Length
- 431 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,2-dialkylglycine decarboxylase
- EC
- 4.1.1.64
- UniProt
- P16932
- Ligands
- PLP, NA, CA
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,2-dialkylglycine decarboxylase (EC 4.1.1.64) | protein | 431 | 39% helix, 19% strand | P16932 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- NA · Sodium ion · metal · chains A
- CA · Calcium 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.54 | 0.77 | 24 | empty |
| 2 | 140 | 0.44 | 0.76 | 28 | PLP, MES |
| 3 | 74 | 0.44 | 0.81 | 22 | empty |
| 4 | 147 | 0.40 | 0.73 | 24 | empty |
| 5 | 89 | 0.38 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1ZOB · Crystal structure of dialkylglycine decarboxylases bound with calcium ion · 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 1ZOB · PDBe 1ZOB · UniProt P16932
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