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
- 5WGG
- Type
- protein
- Length
- 451 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Radical SAM domain protein; Ctea
- UniProt
- A3DDW1, A3DDW2
- Ligands
- SF4, SAM, CA
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Radical SAM domain protein | protein | 440 | 43% helix, 16% strand | A3DDW1 |
| B | Ctea | protein | 11 | 0% helix, 27% strand | A3DDW2 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.85 | 0.86 | 101 | SF4, SAM |
| 2 | 119 | 0.47 | 0.79 | 26 | empty |
| 3 | 116 | 0.37 | 0.74 | 30 | empty |
| 4 | 54 | 0.37 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 822 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5WGG · 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
- Every structure of UniProt A3DDW2
- Elsewhere: RCSB PDB 5WGG · PDBe 5WGG · UniProt A3DDW1 · UniProt A3DDW2
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