Research workbench
SARS-cov-2 RNA-dependent RNA polymerase in complex with cofactors
Analyse SARS-cov-2 RNA-dependent RNA polymerase in complex with cofactors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M71
- Type
- protein
- Length
- 1,085 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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
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