Research workbench
Crystal structure of the flavin oxygenase with cofactor and substrate bound involved in folate catabolism
Analyse Crystal structure of the flavin oxygenase with cofactor and substrate bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V43
- Type
- protein
- Length
- 932 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD/FMN-containing dehydrogenase
- UniProt
- A9D9D1
- Ligands
- LUZ, FAD
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | FAD/FMN-containing dehydrogenase | protein | 466 | 32% helix, 23% strand | A9D9D1 |
Ligands and binding sites
- LUZ · pteridine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.85 | 0.94 | 55 | LUZ, FAD |
| 2 | 340 | 0.84 | 0.93 | 50 | LUZ, FAD |
| 3 | 170 | 0.81 | 0.97 | 40 | empty |
| 4 | 65 | 0.73 | 0.98 | 20 | empty |
| 5 | 63 | 0.72 | 0.97 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1676 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 6V43 · Crystal structure of the flavin oxygenase with cofactor and substrate bound involved in… · 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 A9D9D1
- Elsewhere: RCSB PDB 6V43 · PDBe 6V43 · UniProt A9D9D1
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