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The crystal structure of dfoj, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen erwinia amylovora
Analyse The crystal structure of dfoj, the desferrioxamine biosynthetic pathway lysine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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