Research workbench
The crystal structure of a Radical SAM Enzyme DesII
Analyse The crystal structure of a Radical SAM Enzyme DesII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8HZY
- Type
- protein
- Length
- 920 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.03979
- Source
- Homo sapiens
- Molecule
- DesII
- Ligands
- SF4, MET
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.03979 · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DesII | protein | 462 | 48% helix, 11% strand | — |
| B | DesII | protein | 458 | 52% helix, 10% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.77 | 0.79 | 74 | SF4 |
| 2 | 1018 | 0.76 | 0.78 | 78 | MET, SF4 |
| 3 | 73 | 0.36 | 0.77 | 16 | empty |
| 4 | 60 | 0.31 | 0.75 | 18 | empty |
| 5 | 80 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 306 Ų buried · 9 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8HZY · PDBe 8HZY
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