MolNFT v1 · #169898 · protein + RNA
SARS-cov-2 RDRP/RNA complex
6XQB · RNA-directed RNA polymerase: “SARS-cov-2 RDRP/RNA complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.82). MolNFT v1 #169898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XQB
- Type
- protein + RNA
- Length
- 1,023 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7; RNA…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 801 | 42% helix, 13% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 114 | 36% helix, 21% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 62 | 76% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 31 | 81% helix, 0% strand | P0DTD1 |
| E | RNA (5'-R(*GP*UP*GP*GP*GP*CP*CP*CP*A)-3') | rna | 7 | — | — |
| F | RNA (5'-R(*GP*UP*GP*GP*GP*CP*CP*CP*A)-3') | rna | 8 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.82 | 0.90 | 54 | empty |
| 2 | 171 | 0.79 | 0.95 | 45 | empty |
| 3 | 173 | 0.79 | 0.94 | 32 | empty |
| 4 | 1119 | 0.75 | 0.78 | 83 | empty |
| 5 | 69 | 0.74 | 0.97 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2169 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 830 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–D · 645 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 610 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 573 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6XQB · SARS-CoV-2 RdRp/RNA complex · 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 6XQB · PDBe 6XQB · UniProt P0DTD1
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