MolNFT v1 · #29556 · protein
The crystal structure of dialkylglycine decarboxylase complex with pyridoxamine 5-phosphate
1ZC9 · 2,2-dialkylglycine decarboxylase: “The crystal structure of dialkylglycine decarboxylase complex with pyridoxamine 5-phosphate”. X-ray diffraction, 3 ligands (PMP, K, NA), 4 pockets (best druggability 0.53). MolNFT v1 #29556 on…
- PDB
- 1ZC9
- 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
- PMP, K, NA
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,2-dialkylglycine decarboxylase (EC 4.1.1.64) | protein | 431 | 40% helix, 19% strand | P16932 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A
- K · Potassium ion · metal · chains A
- NA · Sodium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.53 | 0.78 | 37 | PMP |
| 2 | 204 | 0.51 | 0.76 | 25 | empty |
| 3 | 187 | 0.45 | 0.74 | 27 | empty |
| 4 | 64 | 0.36 | 0.78 | 15 | empty |
Compared structures
- 1ZC9 · The crystal structure of dialkylglycine decarboxylase complex with pyridoxamine… · 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 1ZC9 · PDBe 1ZC9 · UniProt P16932
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