MolNFT v1 · #119170 · protein
F206W mutant of FAD synthetase from corynebacterium ammoniagenes
5FNZ · Riboflavin biosynthesis protein ribf: “F206W mutant of FAD synthetase from corynebacterium ammoniagenes”. X-ray diffraction, 2 ligands (PPV, SO4), 9 pockets (best druggability 0.79). MolNFT v1 #119170 on GenesisL1: 3D structure…
- PDB
- 5FNZ
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin biosynthesis protein ribf
- EC
- 2.7.1.26, 2.7.7.2
- UniProt
- Q59263
- Ligands
- PPV, SO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin biosynthesis protein ribf (EC 2.7.1.26, 2.7.7.2) | protein | 328 | 30% helix, 29% strand | Q59263 |
| B | Riboflavin biosynthesis protein ribf (EC 2.7.1.26, 2.7.7.2) | protein | 333 | 29% helix, 29% strand | Q59263 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.79 | 0.81 | 106 | SO4 |
| 2 | 350 | 0.64 | 0.79 | 42 | PPV |
| 3 | 337 | 0.63 | 0.79 | 40 | PPV |
| 4 | 219 | 0.58 | 0.80 | 40 | empty |
| 5 | 224 | 0.50 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 833 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5FNZ · F206W mutant of FAD synthetase from Corynebacterium ammoniagenes · the same entry in another collection · chain A against A, TM-score 1.00
- Q59263 · AlphaFold monomer V2.0 prediction for bifunctional riboflavin KINASE/FMN… · 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 Q59263
- Elsewhere: RCSB PDB 5FNZ · PDBe 5FNZ · UniProt Q59263
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