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Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2
Analyse Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VYO
- Type
- protein
- Length
- 499 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- P0DTC9
- Ligands
- ZN, CL
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 124 | 2% helix, 23% strand | P0DTC9 |
| B, C, D | Nucleoprotein | protein | 125 | 2% helix, 26% strand | P0DTC9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, D, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.68 | 0.84 | 36 | CL, MES |
| 2 | 238 | 0.66 | 0.84 | 39 | CL, MES |
| 3 | 300 | 0.59 | 0.78 | 40 | MES |
| 4 | 255 | 0.58 | 0.79 | 29 | MES |
| 5 | 65 | 0.33 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 606 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 567 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 414 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 407 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6VYO · Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS… · 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 P0DTC9
- Elsewhere: RCSB PDB 6VYO · PDBe 6VYO · UniProt P0DTC9
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