MolNFT v2 · #157570 · protein
SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors
6M71 · RNA-directed RNA polymerase: “SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors”. Electron microscopy at 2.9, 17 pockets (best druggability 0.64). MolNFT v2 #157570 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6M71
- Type
- protein
- Length
- 1,085 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 7; Non-structural protein 8
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Pockets
- 17 · best druggability 0.64
Structure
electron microscopy · resolution 2.9 · 4 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 859 | 43% helix, 15% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 70 | 71% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 43 | 56% helix, 5% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 113 | 28% helix, 19% strand | P0DTD1 |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.64 | 0.79 | 43 | empty |
| 2 | 437 | 0.59 | 0.75 | 49 | empty |
| 3 | 246 | 0.54 | 0.77 | 33 | empty |
| 4 | 65 | 0.54 | 0.87 | 24 | empty |
| 5 | 234 | 0.51 | 0.75 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2384 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1233 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 827 Ų buried · 6 hydrogen bonds · protein-protein
- C–B · 155 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 122 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6M71 · SARS-cov-2 RNA-dependent RNA polymerase in complex with cofactors · 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 6M71 · PDBe 6M71 · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.