MolNFT v1 · #174370 · protein
SARS-cov-2 RNA-dependent RNA polymerase in complex with cofactors in reduced condition
7BTF · RNA-directed RNA polymerase: “SARS-cov-2 RNA-dependent RNA polymerase in complex with cofactors in reduced condition”. Electron microscopy, 1 ligand (ZN), 14 pockets (best druggability 0.70). MolNFT v1 #174370 on GenesisL1: 3D…
- PDB
- 7BTF
- Type
- protein
- Length
- 1,213 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
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.70
Structure
electron microscopy · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 915 | 41% helix, 17% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 68 | 72% helix, 0% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 126 | 34% helix, 24% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 104 | 35% helix, 29% 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.70 | 0.81 | 50 | empty |
| 2 | 259 | 0.60 | 0.80 | 40 | empty |
| 3 | 233 | 0.56 | 0.78 | 32 | empty |
| 4 | 60 | 0.54 | 0.88 | 20 | empty |
| 5 | 80 | 0.54 | 0.85 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2760 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1264 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 834 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 156 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 151 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BTF · SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors in reduced condition · 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 7BTF · PDBe 7BTF · UniProt P0DTD1
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