Research workbench
Oridonin-bound SARS-cov-2 NSP9
Analyse Oridonin-bound SARS-cov-2 NSP9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N3K
- Type
- protein
- Length
- 989 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 9
- UniProt
- P0DTD1
- Ligands
- ODN, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H | Non-structural protein 9 | protein | 124 | 11% helix, 50% strand | P0DTD1 |
| G | Non-structural protein 9 | protein | 121 | 12% helix, 51% strand | P0DTD1 |
Ligands and binding sites
- ODN · (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14r, 16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.77 | 0.79 | 82 | ODN |
| 2 | 210 | 0.45 | 0.73 | 28 | empty |
| 3 | 90 | 0.40 | 0.77 | 17 | empty |
| 4 | 86 | 0.38 | 0.76 | 19 | empty |
| 5 | 91 | 0.35 | 0.75 | 19 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1135 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1126 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1111 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1111 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 317 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 7N3K · Oridonin-bound SARS-CoV-2 Nsp9 · 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 P0DTD1
- Elsewhere: RCSB PDB 7N3K · PDBe 7N3K · UniProt P0DTD1
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