Research workbench
Cryoem reconstruction of cowpea mosaic virus (cpmv) bound to an affimer reagent
Analyse Cryoem reconstruction of cowpea mosaic virus (cpmv) bound to an affimer reagent in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QOZ
- Type
- protein
- Length
- 2,307 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA2 polyprotein; Cowpea mosaic virus large subunit; Affimer binding protein
- UniProt
- P03599
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, H | RNA2 polyprotein | protein | 189 | 6% helix, 44% strand | P03599 |
| B, E, G, I | Cowpea mosaic virus large subunit | protein | 368 | 10% helix, 40% strand | P03599 |
| C | Affimer binding protein | protein | 79 | 24% helix, 53% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.79 | 0.82 | 82 | empty |
| 2 | 709 | 0.75 | 0.80 | 68 | empty |
| 3 | 217 | 0.66 | 0.84 | 24 | empty |
| 4 | 249 | 0.63 | 0.81 | 38 | empty |
| 5 | 213 | 0.63 | 0.82 | 28 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1783 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1781 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 1781 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1779 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 1694 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6QOZ · CryoEM reconstruction of Cowpea Mosaic Virus (CPMV) bound to an Affimer reagent · 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 P03599
- Elsewhere: RCSB PDB 6QOZ · PDBe 6QOZ · UniProt P03599
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.