Research workbench
Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor 3-pkb
Analyse Crystal structure of benzoylformate decarboxylase in complex with the pyridyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F6E
- 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
- 8PA, MG
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 525 | 40% helix, 18% strand | P20906 |
Ligands and binding sites
- 8PA · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1S,2E)-1-hydroxy-3-pyridin-3-ylprop-2-en-1-yl]-4-methyl-1,3-thiazol-3-ium · ligand · chains X
- MG · Magnesium ion · metal
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 | 467 | 0.66 | 0.78 | 57 | empty |
| 2 | 204 | 0.54 | 0.79 | 32 | empty |
| 3 | 54 | 0.27 | 0.74 | 16 | empty |
Compared structures
- 3F6E · Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor… · the same entry in another collection · chain X against X, TM-score 1.00
- P20906 · AlphaFold monomer V2.0 prediction for benzoylformate decarboxylase (P20906) · a predicted model of the same protein · chain X 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 3F6E · PDBe 3F6E · UniProt P20906
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