Research workbench
Structure of the RNA-dependent RNA polymerase from SARS-cov-2
Analyse Structure of the RNA-dependent RNA polymerase from SARS-cov-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BW4
- Type
- protein
- Length
- 1,078 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.71
Structure
electron microscopy · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 811 | 43% helix, 14% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 115 | 36% helix, 26% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 65 | 74% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 87 | 38% helix, 21% strand | P0DTD1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.71 | 0.80 | 65 | empty |
| 2 | 190 | 0.61 | 0.83 | 38 | empty |
| 3 | 76 | 0.59 | 0.88 | 24 | empty |
| 4 | 100 | 0.57 | 0.86 | 22 | empty |
| 5 | 244 | 0.54 | 0.77 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2596 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 960 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 742 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 64 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BW4 · Structure of the RNA-dependent RNA polymerase from SARS-CoV-2 · 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 7BW4 · PDBe 7BW4 · UniProt P0DTD1
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