Research workbench
Cryo-EM structure of giant freshwater prawn macrobrachium rosenbergii nodavirus (mrnv) semi-empty vlp
Analyse Cryo-EM structure of giant freshwater prawn macrobrachium rosenbergii nodavirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JJC
- Type
- protein
- Length
- 602 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q15BP6
- Ligands
- CA
- Pockets
- 1 · best druggability 0.34
Structure
electron microscopy · 2 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid protein | protein | 193 | 11% helix, 35% strand | Q15BP6 |
| C | Capsid protein | protein | 216 | 14% helix, 33% strand | Q15BP6 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.34 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1604 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1301 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1270 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6JJC · Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV)… · 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 Q15BP6
- Elsewhere: RCSB PDB 6JJC · PDBe 6JJC · UniProt Q15BP6
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