MolNFT v1 · #137569 · protein
Crystal structure of viperin with bound [4FE-4S] cluster, 5'- deoxyadenosine, and L-methionine
5VSM · Radical S-adenosyl methionine domain-containing protein 2: “Crystal structure of viperin with bound [4FE-4S] cluster, 5'- deoxyadenosine, and L-methionine”. X-ray diffraction, 3 ligands (SF4, 5AD, MET), 5 pockets (best druggability…
- PDB
- 5VSM
- Type
- protein
- Length
- 511 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, 5AD, MET
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Radical S-adenosyl methionine domain-containing protein 2 | protein | 258 | 39% helix, 17% strand | Q8CBB9 |
| B | Radical S-adenosyl methionine domain-containing protein 2 | protein | 253 | 39% helix, 17% strand | Q8CBB9 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, B
- MET · Methionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.81 | 0.88 | 59 | SF4, 5AD, MET |
| 2 | 419 | 0.79 | 0.87 | 53 | SF4, 5AD, MET |
| 3 | 97 | 0.49 | 0.82 | 28 | empty |
| 4 | 113 | 0.39 | 0.76 | 19 | empty |
| 5 | 51 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 893 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5VSM · Crystal structure of viperin with bound [4Fe-4S] cluster, 5'-deoxyadenosine, and… · 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 B 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 5VSM · PDBe 5VSM · UniProt Q8CBB9
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