Research workbench
Schmallenberg virus nucleoprotein-RNA complex
Analyse Schmallenberg virus nucleoprotein-RNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JNG
- Type
- protein + RNA
- Length
- 929 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (42-mer); Nucleocapsid protein
- UniProt
- H2AM13
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | RNA (42-mer) | rna | 42 | — | — |
| A | Nucleocapsid protein | protein | 226 | 53% helix, 8% strand | H2AM13 |
| B | Nucleocapsid protein | protein | 214 | 53% helix, 7% strand | H2AM13 |
| C | Nucleocapsid protein | protein | 224 | 47% helix, 6% strand | H2AM13 |
| D | Nucleocapsid protein | protein | 223 | 50% helix, 5% strand | H2AM13 |
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.81 | 0.96 | 32 | empty |
| 2 | 171 | 0.80 | 0.96 | 35 | empty |
| 3 | 178 | 0.79 | 0.95 | 36 | empty |
| 4 | 158 | 0.79 | 0.96 | 29 | empty |
| 5 | 980 | 0.76 | 0.79 | 74 | empty |
Interfaces
8 interfaces between chains.
- L–D · 1505 Ų buried · 31 hydrogen bonds · protein-nucleic
- L–B · 1505 Ų buried · 33 hydrogen bonds · protein-nucleic
- L–A · 1496 Ų buried · 28 hydrogen bonds · protein-nucleic
- L–C · 1297 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 1185 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4JNG · Schmallenberg virus nucleoprotein-RNA complex · the same entry in another collection · chain L against L, 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 H2AM13
- Elsewhere: RCSB PDB 4JNG · PDBe 4JNG · UniProt H2AM13
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