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Structure of the SARS-cov-2 N protein RNA-binding domain bound to single-domain antibody C2
Analyse Structure of the SARS-cov-2 N protein RNA-binding domain bound to single-domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N0R
- Type
- protein
- Length
- 500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; Single-domain antibody C2
- UniProt
- P0DTC9
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoprotein | protein | 127 | 2% helix, 24% strand | P0DTC9 |
| C, D | Single-domain antibody C2 | protein | 123 | 10% helix, 44% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.72 | 0.82 | 39 | SO4 |
| 2 | 146 | 0.50 | 0.79 | 28 | empty |
| 3 | 103 | 0.43 | 0.78 | 18 | empty |
| 4 | 124 | 0.40 | 0.75 | 17 | empty |
| 5 | 89 | 0.34 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–D · 823 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 821 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 670 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 162 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 143 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7N0R · Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody… · 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 7N0R · PDBe 7N0R · UniProt P0DTC9
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