Research workbench
Structural insights into thioether bond formation in the biosynthesis of sactipeptides
Analyse Structural insights into thioether bond formation in the biosynthesis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WHY
- Type
- protein
- Length
- 839 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Radical SAM domain protein
- UniProt
- A3DDW1
- Ligands
- SF4, SAM, CA
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Radical SAM domain protein | protein | 418 | 41% helix, 16% strand | A3DDW1 |
| B | Radical SAM domain protein | protein | 421 | 43% helix, 17% strand | A3DDW1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 5 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 | 863 | 0.85 | 0.87 | 89 | SF4, SAM |
| 2 | 1160 | 0.83 | 0.84 | 91 | SF4, SAM |
| 3 | 195 | 0.57 | 0.80 | 36 | CA |
| 4 | 281 | 0.53 | 0.76 | 39 | CA |
| 5 | 112 | 0.53 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 713 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5WHY · Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides · 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 A3DDW1
- Elsewhere: RCSB PDB 5WHY · PDBe 5WHY · UniProt A3DDW1
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