MolNFT v1 · #106108 · protein
Crystal structure of P domain of snow mountain norovirus
4RPB · Capsid protein VP1: “Crystal structure of P domain of snow mountain norovirus”. X-ray diffraction, 3 pockets (best druggability 0.78). MolNFT v1 #106108 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RPB
- Type
- protein
- Length
- 900 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- K7X601
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Capsid protein VP1 | protein | 300 | 6% helix, 36% strand | K7X601 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.78 | 0.80 | 122 | EDO |
| 2 | 126 | 0.68 | 0.90 | 25 | EDO |
| 3 | 567 | 0.65 | 0.76 | 66 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 1941 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 252 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4RPB · Crystal Structure of P Domain of Snow Mountain Norovirus · 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 K7X601
- Elsewhere: RCSB PDB 4RPB · PDBe 4RPB · UniProt K7X601
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