MolNFT v1 · #161068 · protein
Crystal structure of mouse viperin bound to cytidine triphosphate and S-adenosylhomocysteine
6Q2P · Radical S-adenosyl methionine domain-containing protein 2: “Crystal structure of mouse viperin bound to cytidine triphosphate and S-adenosylhomocysteine”. X-ray diffraction, 4 ligands (SF4, SAH, CTP), 5 pockets (best druggability…
- PDB
- 6Q2P
- Type
- protein
- Length
- 584 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, CTP, CL
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Radical S-adenosyl methionine domain-containing protein 2 | protein | 291 | 37% helix, 18% strand | Q8CBB9 |
| B | Radical S-adenosyl methionine domain-containing protein 2 | protein | 293 | 36% 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
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.86 | 0.95 | 52 | SF4, SAH, CTP |
| 2 | 370 | 0.85 | 0.94 | 56 | SF4, SAH, CTP |
| 3 | 198 | 0.76 | 0.91 | 33 | empty |
| 4 | 90 | 0.53 | 0.84 | 23 | empty |
| 5 | 79 | 0.32 | 0.74 | 29 | CL |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Q2P · Crystal structure of mouse viperin bound to cytidine triphosphate 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 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 Q8CBB9
- Elsewhere: RCSB PDB 6Q2P · PDBe 6Q2P · UniProt Q8CBB9
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