MolNFT v2 · #225881 · protein
Structure of SADS-CoV Virus Nucleocapsid Protein
8YM1 · nucleocapsid phosphoprotein: “Structure of SADS-CoV Virus Nucleocapsid Protein”. X-ray diffraction at 1.9, 8 pockets (best druggability 0.70). MolNFT v2 #225881 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8YM1
- Type
- protein
- Length
- 831 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Swine acute diarrhea syndrome coronavirus
- Molecule
- nucleocapsid phosphoprotein
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.9 · 6 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | nucleocapsid phosphoprotein | protein | 102 | 35% helix, 23% strand | — |
| B | nucleocapsid phosphoprotein | protein | 107 | 36% helix, 21% strand | — |
| C | nucleocapsid phosphoprotein | protein | 104 | 36% helix, 22% strand | — |
| E | nucleocapsid phosphoprotein | protein | 107 | 36% helix, 21% strand | — |
| F, H | nucleocapsid phosphoprotein | protein | 103 | 43% helix, 22% strand | — |
| G | nucleocapsid phosphoprotein | protein | 103 | 40% helix, 22% strand | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.70 | 0.75 | 101 | empty |
| 2 | 428 | 0.60 | 0.75 | 28 | empty |
| 3 | 360 | 0.56 | 0.74 | 26 | empty |
| 4 | 130 | 0.40 | 0.75 | 18 | empty |
| 5 | 134 | 0.39 | 0.74 | 23 | empty |
Interfaces
13 interfaces between chains.
- E–G · 2803 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 2789 Ų buried · 52 hydrogen bonds · protein-protein
- A–F · 2758 Ų buried · 51 hydrogen bonds · protein-protein
- E–H · 329 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 295 Ų buried · 2 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8YM1 · PDBe 8YM1
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