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Crystal structure of rift valley fever virus nucleocapsid protein pentamer bound to single-stranded RNA
Analyse Crystal structure of rift valley fever virus nucleocapsid protein pentamer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H5O
- Type
- protein + RNA
- Length
- 2,508 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleocapsid protein; 35-mer POLY(U) RNA
- UniProt
- D3K5I7
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleocapsid protein | protein | 242 | 64% helix, 3% strand | D3K5I7 |
| B, C, D, E, F, G, H, I, J | Nucleocapsid protein | protein | 244 | 64% helix, 3% strand | D3K5I7 |
| K, L | 35-mer POLY(U) RNA | rna | 35 | — | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.75 | 0.78 | 91 | empty |
| 2 | 50 | 0.69 | 0.98 | 17 | empty |
| 3 | 272 | 0.65 | 0.82 | 42 | empty |
| 4 | 188 | 0.64 | 0.84 | 21 | empty |
| 5 | 357 | 0.63 | 0.79 | 44 | empty |
Interfaces
27 interfaces between chains.
- A–D · 1713 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1696 Ų buried · 19 hydrogen bonds · protein-protein
- H–J · 1694 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 1691 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1690 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4H5O · Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Pentamer Bound to… · 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 D3K5I7
- Elsewhere: RCSB PDB 4H5O · PDBe 4H5O · UniProt D3K5I7
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