MolNFT v1 · #96805 · protein
Crystal structure of the SER26THR mutant of benzoylformate decarboxylase from pseudomonas putida
4JUD: “Crystal structure of the SER26THR mutant of benzoylformate decarboxylase from pseudomonas putida”. X-ray diffraction, 3 ligands (TZD, MG, CA), 4 pockets (best druggability 0.61). MolNFT v1 #96805 on GenesisL1: 3D structure, binding…
- PDB
- 4JUD
- 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, MG, CA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 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 X
- MG · Magnesium ion · metal · chains X
- CA · Calcium ion · metal · chains X
- GOL · Glycerol · additive · 5 copies · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.61 | 0.77 | 44 | TZD, CA |
| 2 | 198 | 0.55 | 0.79 | 31 | empty |
| 3 | 52 | 0.52 | 0.88 | 21 | GOL |
| 4 | 80 | 0.36 | 0.76 | 16 | empty |
Compared structures
- 4JUD · Crystal Structure of the Ser26Thr mutant of Benzoylformate Decarboxylase from Pseudomonas… · 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 4JUD · PDBe 4JUD · UniProt P20906
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