MolNFT v1 · #129047 · protein
The crystal structure of dfoa bound to FAD and NADP; the desferrioxamine biosynthetic pathway cadaverine monooxygenase from the fire blight disease pathogen erwinia amylovora
5O8R · L-lysine 6-monooxygenase involved in desferrioxamine…: “The crystal structure of dfoa bound to FAD and NADP; the desferrioxamine biosynthetic pathway cadaverine…”. X-ray diffraction, 2 ligands (FAD, NAP), 4 pockets (best…
- PDB
- 5O8R
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis
- EC
- 1.14.13.59
- UniProt
- D4I246
- Ligands
- FAD, NAP
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis (EC 1.14.13.59) | protein | 427 | 30% helix, 25% strand | D4I246 |
| B | L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis (EC 1.14.13.59) | protein | 427 | 30% helix, 22% strand | D4I246 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.84 | 0.85 | 103 | FAD, NAP |
| 2 | 1167 | 0.83 | 0.83 | 108 | FAD, NAP |
| 3 | 74 | 0.38 | 0.78 | 16 | empty |
| 4 | 50 | 0.26 | 0.74 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 987 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5O8R · The crystal structure of DfoA bound to FAD and NADP; the desferrioxamine biosynthetic… · 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 D4I246
- Elsewhere: RCSB PDB 5O8R · PDBe 5O8R · UniProt D4I246
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