MolNFT v1 · #189621 · protein
Crystal structure of the N-terminal domain of SARS-cov-2 nucleocapsid protein
7VNU · Nucleoprotein: “Crystal structure of the N-terminal domain of SARS-cov-2 nucleocapsid protein”. X-ray diffraction, 5 pockets (best druggability 0.78). MolNFT v1 #189621 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VNU
- Type
- protein
- Length
- 507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- P0DTC9
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoprotein | protein | 128 | 2% helix, 27% strand | P0DTC9 |
| C | Nucleoprotein | protein | 127 | 5% helix, 24% strand | P0DTC9 |
| D | Nucleoprotein | protein | 124 | 5% helix, 27% strand | P0DTC9 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.78 | 0.80 | 92 | empty |
| 2 | 469 | 0.67 | 0.79 | 61 | empty |
| 3 | 192 | 0.66 | 0.85 | 30 | empty |
| 4 | 168 | 0.55 | 0.80 | 25 | empty |
| 5 | 50 | 0.25 | 0.73 | 11 | empty |
Interfaces
6 interfaces between chains.
- B–C · 715 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 485 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 389 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 120 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7VNU · Crystal structure of the N-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 7VNU · PDBe 7VNU · UniProt P0DTC9
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