MolNFT v1 · #138763 · protein
Cryo-EM structure for hepatitis a virus empty particle
5WTF · VP1: “Cryo-EM structure for hepatitis a virus empty particle”. Electron microscopy, 6 pockets (best druggability 0.56). MolNFT v1 #138763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WTF
- Type
- protein
- Length
- 673 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP0; VP3
- Pockets
- 6 · best druggability 0.56
Structure
electron microscopy · 3 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 224 | 8% helix, 34% strand | — |
| B | VP0 | protein | 203 | 7% helix, 39% strand | — |
| C | VP3 | protein | 246 | 8% helix, 31% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.56 | 0.77 | 37 | empty |
| 2 | 57 | 0.32 | 0.77 | 21 | empty |
| 3 | 77 | 0.32 | 0.74 | 20 | empty |
| 4 | 55 | 0.27 | 0.74 | 13 | empty |
| 5 | 66 | 0.27 | 0.72 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3488 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 1447 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1137 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5WTF · Cryo-EM structure for Hepatitis A virus empty particle · 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
- Elsewhere: RCSB PDB 5WTF · PDBe 5WTF
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