Research workbench
Crystal structure of the C-terminal domain of SARS-cov-2 nucleocapsid protein
Analyse Crystal structure of the C-terminal domain of SARS-cov-2 nucleocapsid protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C22
- Type
- protein
- Length
- 442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- P0DTC9
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 109 | 40% helix, 20% strand | P0DTC9 |
| B | Nucleoprotein | protein | 113 | 42% helix, 19% strand | P0DTC9 |
| C | Nucleoprotein | protein | 112 | 37% helix, 21% strand | P0DTC9 |
| D | Nucleoprotein | protein | 108 | 39% helix, 21% strand | P0DTC9 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.53 | 0.74 | 35 | PEG |
| 2 | 88 | 0.40 | 0.78 | 14 | empty |
| 3 | 66 | 0.31 | 0.75 | 16 | ACT |
| 4 | 60 | 0.30 | 0.75 | 15 | empty |
| 5 | 57 | 0.29 | 0.75 | 16 | ACT |
Interfaces
3 interfaces between chains.
- C–D · 2700 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2672 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7C22 · Crystal structure of the C-terminal domain of SARS-CoV-2 nucleocapsid protein · 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 7C22 · PDBe 7C22 · UniProt P0DTC9
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