MolNFT v1 · #116465 · protein
Benzoylformate decarboxylase from pseudomonas putida
5DEI: “Benzoylformate decarboxylase from pseudomonas putida”. X-ray diffraction, 4 ligands (BCT, TPP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #116465 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DEI
- Type
- protein
- Length
- 2,096 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoylformate decarboxylase
- EC
- 4.1.1.7
- UniProt
- P20906
- Ligands
- BCT, TPP, MG, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 524 | 39% helix, 19% strand | P20906 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 4 copies · chains A, C, B, D
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 8 copies · chains A, C, D, B
- CA · Calcium ion · metal · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.85 | 0.93 | 74 | empty |
| 2 | 330 | 0.82 | 0.92 | 60 | empty |
| 3 | 206 | 0.80 | 0.94 | 37 | empty |
| 4 | 206 | 0.79 | 0.94 | 44 | empty |
| 5 | 519 | 0.78 | 0.85 | 66 | BCT, TPP, CA |
Interfaces
6 interfaces between chains.
- B–D · 3595 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 3572 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1751 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1747 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 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 5DEI · PDBe 5DEI · UniProt P20906
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