Research workbench
Crystal structure of benzoylformate decarboxylase mutant L403S
Analyse Crystal structure of benzoylformate decarboxylase mutant L403S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GM1
- 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
- TZD, CA, NA
- Pockets
- 3 · best druggability 0.59
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 | 525 | 39% helix, 18% strand | P20906 |
Ligands and binding sites
- TZD · 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-2-oxo-2,3-dihydro-1,3-thiazol-5-yl}ethyl trihydrogen diphosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 2 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 | 328 | 0.59 | 0.77 | 44 | CA, TZD |
| 2 | 206 | 0.55 | 0.79 | 34 | empty |
| 3 | 83 | 0.38 | 0.77 | 16 | empty |
Compared structures
- 4GM1 · Crystal Structure of Benzoylformate Decarboxylase Mutant L403S · 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 4GM1 · PDBe 4GM1 · UniProt P20906
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