MolNFT v1 · #161780 · protein
Cryoem reconstruction of cowpea mosaic virus (cpmv) bound to an affimer reagent
6QOZ · RNA2 polyprotein: “Cryoem reconstruction of cowpea mosaic virus (cpmv) bound to an affimer reagent”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #161780 on GenesisL1: 3D structure, binding sites and pockets…
- 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
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