Research workbench
Radical SAM 1,2-diol dehydratase APRD4 in complex with its substrate paromamine
Analyse Radical SAM 1,2-diol dehydratase APRD4 in complex with its substrate paromamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FD2
- Type
- protein
- Length
- 907 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative apramycin biosynthetic oxidoreductase 4
- UniProt
- Q2MFI7
- Ligands
- D5E, SF4, MET, 5AD
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Putative apramycin biosynthetic oxidoreductase 4 | protein | 453 | 41% helix, 16% strand | Q2MFI7 |
| A | Putative apramycin biosynthetic oxidoreductase 4 | protein | 454 | 41% helix, 17% strand | Q2MFI7 |
Ligands and binding sites
- D5E · paromamine · ligand · 2 copies · chains B, A
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, A
- MET · Methionine · ligand · 2 copies · chains B, A
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.84 | 0.88 | 67 | D5E, SF4, MET, 5AD |
| 2 | 672 | 0.83 | 0.87 | 67 | D5E, SF4, MET, 5AD |
| 3 | 158 | 0.81 | 0.97 | 38 | empty |
| 4 | 129 | 0.79 | 0.97 | 36 | empty |
| 5 | 1067 | 0.77 | 0.79 | 127 | empty |
Interfaces
1 interface between chains.
- B–A · 634 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6FD2 · Radical SAM 1,2-diol dehydratase AprD4 in complex with its substrate paromamine · 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 Q2MFI7
- Elsewhere: RCSB PDB 6FD2 · PDBe 6FD2 · UniProt Q2MFI7
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