MolNFT v1 · #128933 · protein
The crystal structure of dfoj, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen erwinia amylovora
5O5C · Putative decarboxylase involved in desferrioxamine…: “The crystal structure of dfoj, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire…”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability…
- PDB
- 5O5C
- Type
- protein
- Length
- 2,786 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative decarboxylase involved in desferrioxamine biosynthesis
- EC
- 4.1.1.-
- UniProt
- D4I245
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative decarboxylase involved in desferrioxamine biosynthesis (EC 4.1.1.-) | protein | 464 | 51% helix, 15% strand | D4I245 |
| B | Putative decarboxylase involved in desferrioxamine biosynthesis (EC 4.1.1.-) | protein | 468 | 50% helix, 15% strand | D4I245 |
| C | Putative decarboxylase involved in desferrioxamine biosynthesis (EC 4.1.1.-) | protein | 462 | 49% helix, 15% strand | D4I245 |
| D | Putative decarboxylase involved in desferrioxamine biosynthesis (EC 4.1.1.-) | protein | 468 | 50% helix, 15% strand | D4I245 |
| E | Putative decarboxylase involved in desferrioxamine biosynthesis (EC 4.1.1.-) | protein | 457 | 51% helix, 15% strand | D4I245 |
| F | Putative decarboxylase involved in desferrioxamine biosynthesis (EC 4.1.1.-) | protein | 467 | 50% helix, 15% strand | D4I245 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.73 | 0.97 | 31 | empty |
| 2 | 679 | 0.70 | 0.77 | 87 | PLP |
| 3 | 50 | 0.69 | 0.98 | 20 | empty |
| 4 | 606 | 0.68 | 0.77 | 66 | PLP |
| 5 | 506 | 0.67 | 0.78 | 75 | PLP |
Interfaces
5 interfaces between chains.
- C–D · 6429 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 6346 Ų buried · 71 hydrogen bonds · protein-protein
- B–F · 531 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 497 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5O5C · The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine… · the same entry in another collection · 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 D4I245
- Elsewhere: RCSB PDB 5O5C · PDBe 5O5C · UniProt D4I245
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