Research workbench
Crystal structure of modular FAD synthetase from corynebacterium ammoniagenes
Analyse Crystal structure of modular FAD synthetase from corynebacterium ammoniagenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X0K
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin biosynthesis protein ribf
- UniProt
- Q59263
- Ligands
- PPV, SO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Riboflavin biosynthesis protein ribf | protein | 338 | 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.79 | 0.82 | 105 | SO4 |
| 2 | 342 | 0.64 | 0.79 | 41 | PPV |
| 3 | 342 | 0.62 | 0.78 | 40 | PPV |
| 4 | 202 | 0.57 | 0.80 | 39 | empty |
| 5 | 190 | 0.54 | 0.79 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 876 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2X0K · Crystal structure of modular 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 2X0K · PDBe 2X0K · UniProt Q59263
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