Research workbench
SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9
Analyse SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7THM
- Type
- protein
- Length
- 1,150 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.18
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- POP, ZN, MN
- Pockets
- 18 · best druggability 0.66
Structure
electron microscopy · resolution 3.18 · 5 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 860 | 42% helix, 14% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 108 | 33% helix, 23% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 37 | 70% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 71 | 32% helix, 25% strand | P0DTD1 |
| G | Non-structural protein 9 | protein | 74 | 11% helix, 22% strand | P0DTD1 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A, G
- ZN · Zinc ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.66 | 0.79 | 49 | empty |
| 2 | 459 | 0.64 | 0.77 | 54 | empty |
| 3 | 127 | 0.59 | 0.85 | 28 | empty |
| 4 | 153 | 0.58 | 0.83 | 30 | empty |
| 5 | 200 | 0.57 | 0.80 | 38 | MN, POP |
Interfaces
6 interfaces between chains.
- A–B · 2265 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 844 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 764 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 507 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7THM · SARS-cov-2 NSP12/7/8 complex with a native N-terminus 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 7THM · PDBe 7THM · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.