Research workbench
Phosphorylation of an active site serine in a thdp-dependent enzyme by phosphonate inactivation
Analyse Phosphorylation of an active site serine in a thdp-dependent enzyme by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FWN
- 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, CA, MG
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 524 | 39% helix, 18% strand | P20906 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · 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 | 405 | 0.64 | 0.78 | 54 | CA, TPP |
| 2 | 190 | 0.52 | 0.78 | 35 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 2FWN · Phosphorylation of an active site serine in a ThDP-dependent enzyme by phosphonate… · 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 2FWN · PDBe 2FWN · UniProt P20906
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