Research workbench
Benzoylformate decarboxylase F464I and A460V mutant from pseudomonas putida
Analyse Benzoylformate decarboxylase F464I and A460V mutant from pseudomonas putida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DGD
- Type
- protein
- Length
- 524 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoylformate decarboxylase
- EC
- 4.1.1.7
- UniProt
- P20906
- Ligands
- TPP, MG, CA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 524 | 40% helix, 18% strand | P20906 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · 3 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.57 | 0.76 | 41 | empty |
| 2 | 214 | 0.55 | 0.79 | 32 | empty |
| 3 | 63 | 0.48 | 0.84 | 20 | TPP |
Compared structures
- 5DGD · Benzoylformate decarboxylase F464I and A460V mutant from Pseudomonas putida · the same entry in another collection · chain A against A, TM-score 1.00
- P20906 · AlphaFold monomer V2.0 prediction for benzoylformate decarboxylase (P20906) · 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 P20906
- Elsewhere: RCSB PDB 5DGD · PDBe 5DGD · UniProt P20906
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