Research workbench
Crystal structure of FAD-dependent C-glycoside oxidase
Analyse Crystal structure of FAD-dependent C-glycoside oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DVE
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6'''-hydroxyparomomycin C oxidase
- EC
- 1.1.3.-
- UniProt
- A0A0M2HFA3
- Ligands
- FAD, SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6'''-hydroxyparomomycin C oxidase (EC 1.1.3.-) | protein | 498 | 25% helix, 23% strand | A0A0M2HFA3 |
| B | 6'''-hydroxyparomomycin C oxidase (EC 1.1.3.-) | protein | 299 | 30% helix, 23% strand | A0A0M2HFA3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.82 | 0.87 | 82 | FAD |
| 2 | 794 | 0.73 | 0.78 | 85 | empty |
| 3 | 190 | 0.54 | 0.79 | 39 | empty |
| 4 | 172 | 0.50 | 0.78 | 32 | empty |
| 5 | 143 | 0.49 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7DVE · Crystal structure of FAD-dependent C-glycoside oxidase · 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 A0A0M2HFA3
- Elsewhere: RCSB PDB 7DVE · PDBe 7DVE · UniProt A0A0M2HFA3
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