MolNFT v1 · #3934 · protein
Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with 5PA
1D7R · Protein (2,2-dialkylglycine decarboxylase (pyruvate)): “Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with 5PA”. X-ray diffraction, 3 ligands (5PA, NA, K), 3 pockets (best druggability 0.59). MolNFT v1 #3934…
- PDB
- 1D7R
- Type
- protein
- Length
- 431 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (2,2-dialkylglycine decarboxylase (pyruvate))
- EC
- 4.1.1.64
- UniProt
- P16932
- Ligands
- 5PA, NA, K
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (2,2-dialkylglycine decarboxylase (pyruvate)) (EC 4.1.1.64) | protein | 431 | 40% helix, 19% strand | P16932 |
Ligands and binding sites
- 5PA · N-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-Y-lmethyl]-1-amino-cyclopropanecarboxylic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
- K · Potassium ion · metal · 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 | 353 | 0.59 | 0.76 | 51 | 5PA |
| 2 | 181 | 0.49 | 0.76 | 23 | empty |
| 3 | 60 | 0.34 | 0.77 | 17 | empty |
Compared structures
- 1D7R · Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with 5PA · 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 1D7R · PDBe 1D7R · UniProt P16932
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