Research workbench
Phosphorylation of an active site threonine in the benzyolformate decarboxylase mutant S26T by phosphonate inactivation
Analyse Phosphorylation of an active site threonine in the benzyolformate decarboxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MPJ
- Type
- protein
- Length
- 525 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, CA, MG, CL
- Pockets
- 2 · best druggability 0.66
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 | 525 | 40% helix, 18% strand | P20906 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.66 | 0.79 | 57 | CA, TPP |
| 2 | 200 | 0.55 | 0.79 | 33 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4MPJ · Phosphorylation of an active site threonine in the benzyolformate decarboxylase mutant… · 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 4MPJ · PDBe 4MPJ · UniProt P20906
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