Research workbench
Crystal structure of viperin with bound [4FE-4S] cluster and S- adenosylhomocysteine (sah)
Analyse Crystal structure of viperin with bound [4FE-4S] cluster and S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VSL
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Radical S-adenosyl methionine domain-containing protein 2
- UniProt
- Q8CBB9
- Ligands
- SF4, SAH
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Radical S-adenosyl methionine domain-containing protein 2 | protein | 262 | 37% helix, 17% strand | Q8CBB9 |
| B | Radical S-adenosyl methionine domain-containing protein 2 | protein | 257 | 38% helix, 18% strand | Q8CBB9 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.82 | 0.89 | 59 | SF4, SAH |
| 2 | 405 | 0.80 | 0.88 | 55 | SF4, SAH |
| 3 | 97 | 0.39 | 0.76 | 16 | empty |
| 4 | 68 | 0.38 | 0.79 | 20 | empty |
| 5 | 65 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 880 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5VSL · Crystal structure of viperin with bound [4Fe-4S] cluster and S-adenosylhomocysteine (SAH) · the same entry in another collection · chain A against A, TM-score 1.00
- Q8CBB9 · AlphaFold monomer V2.0 prediction for radical S-adenosyl methionine domain-containing… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8CBB9
- Elsewhere: RCSB PDB 5VSL · PDBe 5VSL · UniProt Q8CBB9
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