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The crystal structure of dfoc, the desferrioxamine biosynthetic pathway ACETYLTRANSFERASE/NON-ribosomal peptide synthetase (nrps)- independent siderophore (nis) from the fire blight disease pathogen erwinia amylovora
Analyse The crystal structure of dfoc, the desferrioxamine biosynthetic pathway… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O7O
- Type
- protein
- Length
- 1,441 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desferrioxamine siderophore biosynthesis protein dfoc
- UniProt
- D4I247
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Desferrioxamine siderophore biosynthesis protein dfoc | protein | 146 | 30% helix, 38% strand | D4I247 |
| B | Desferrioxamine siderophore biosynthesis protein dfoc | protein | 145 | 30% helix, 38% strand | D4I247 |
| C | Desferrioxamine siderophore biosynthesis protein dfoc | protein | 575 | 42% helix, 20% strand | D4I247 |
| D | Desferrioxamine siderophore biosynthesis protein dfoc | protein | 575 | 44% helix, 20% strand | D4I247 |
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.84 | 0.85 | 112 | empty |
| 2 | 1054 | 0.83 | 0.84 | 103 | empty |
| 3 | 835 | 0.81 | 0.83 | 112 | empty |
| 4 | 476 | 0.64 | 0.77 | 49 | empty |
| 5 | 445 | 0.64 | 0.77 | 50 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1933 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 851 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 780 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 485 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5O7O · The crystal structure of DfoC, the desferrioxamine biosynthetic pathway… · 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 D4I247
- Elsewhere: RCSB PDB 5O7O · PDBe 5O7O · UniProt D4I247
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