MolNFT v2 · #228276 · protein
EVA71 E096A native particle
9F5S · VP0: “EVA71 E096A native particle”. Electron microscopy at 2.5, 1 ligand (SPH), 8 pockets (best druggability 0.74). MolNFT v2 #228276 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 9F5S
- Type
- protein
- Length
- 773 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Enterovirus A71
- Molecule
- VP0; VP3; VP1
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- D4QGA2, D4QGA3, A0A2L1GIK5
- Ligands
- SPH
- Pockets
- 8 · best druggability 0.74
Structure
electron microscopy · resolution 2.5 · 3 distinct chains · 12% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP0 | protein | 293 | 13% helix, 31% strand | D4QGA2 |
| B | VP3 | protein | 242 | 13% helix, 32% strand | D4QGA3 |
| C | VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 238 | 10% helix, 29% strand | A0A2L1GIK5 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.74 | 0.87 | 48 | SPH |
| 2 | 291 | 0.54 | 0.76 | 28 | empty |
| 3 | 140 | 0.49 | 0.78 | 26 | empty |
| 4 | 106 | 0.46 | 0.79 | 21 | empty |
| 5 | 60 | 0.41 | 0.81 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3471 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 2543 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2503 Ų buried · 39 hydrogen bonds · protein-protein
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 D4QGA2
- Every structure of UniProt D4QGA3
- Every structure of UniProt A0A2L1GIK5
- Elsewhere: RCSB PDB 9F5S · PDBe 9F5S · UniProt D4QGA2 · UniProt D4QGA3 · UniProt A0A2L1GIK5
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