Research workbench
FR6-bound SARS-cov-2 NSP9 RNA-replicase
Analyse FR6-bound SARS-cov-2 NSP9 RNA-replicase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KRI
- Type
- protein
- Length
- 377 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 9
- UniProt
- P0DTD1
- Ligands
- X0Y, SO4
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 9 | protein | 127 | 13% helix, 50% strand | P0DTD1 |
| C | Non-structural protein 9 | protein | 123 | 16% helix, 52% strand | P0DTD1 |
Ligands and binding sites
- X0Y · 1,3-dimethyl-1H-pyrrolo[3,4-d]pyrimidine-2,4(3H,6H)-dione · ligand · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- MLI · Malonate ion · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.78 | 0.79 | 113 | empty |
Interfaces
3 interfaces between chains.
- A–C · 300 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 224 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7KRI · FR6-bound SARS-CoV-2 Nsp9 RNA-replicase · 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 7KRI · PDBe 7KRI · UniProt P0DTD1
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