Research workbench
High-resolution Cryo-EM of Fab-labeled human parechovirus 3
Analyse High-resolution Cryo-EM of Fab-labeled human parechovirus 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GV4
- Type
- protein + RNA
- Length
- 925 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens; Human parechovirus 3
- Molecule
- RNA (5'-R(*UP*GP*GP*UP*AP*UP*UP*U)-3'); VP0; VP1; VP3; AT12-015 antibody variable heavy…
- UniProt
- Q8BES5
- Pockets
- 8 · best druggability 0.62
Structure
electron microscopy · resolution 2.8 · 6 distinct chains · 7% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | RNA (5'-R(*UP*GP*GP*UP*AP*UP*UP*U)-3') | rna | 7 | — | — |
| A | VP0 | protein | 256 | 11% helix, 32% strand | Q8BES5 |
| B | VP1 | protein | 195 | 11% helix, 38% strand | Q8BES5 |
| C | VP3 | protein | 241 | 2% helix, 33% strand | Q8BES5 |
| H | AT12-015 antibody variable heavy | protein | 118 | 5% helix, 44% strand | — |
| L | AT12-015 antibody variable light | protein | 108 | 0% helix, 46% strand | — |
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 | 500 | 0.62 | 0.76 | 70 | empty |
| 2 | 277 | 0.58 | 0.78 | 43 | empty |
| 3 | 83 | 0.37 | 0.77 | 18 | empty |
| 4 | 66 | 0.35 | 0.77 | 11 | empty |
| 5 | 50 | 0.34 | 0.79 | 16 | empty |
Interfaces
8 interfaces between chains.
- B–C · 3614 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 1367 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1169 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 922 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 348 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6GV4 · High-resolution cryo-EM of Fab-labeled human parechovirus 3 · 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 Q8BES5
- Elsewhere: RCSB PDB 6GV4 · PDBe 6GV4 · UniProt Q8BES5
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