Research workbench
SARS-cov-2 rdrp with molnupiravir/ nhc in the template strand base- paired with G
Analyse SARS-cov-2 rdrp with molnupiravir/ nhc in the template strand base- paired with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OZV
- Type
- protein + RNA
- Length
- 1,013 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1AB; Non-structural protein 8; Non-structural protein 7; Product…
- UniProt
- P0DTD1
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1AB | protein | 814 | 44% helix, 15% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 115 | 40% helix, 26% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 62 | 81% helix, 0% strand | P0DTD1 |
| P | Product RNA | rna | 10 | — | — |
| T | Template RNA | rna | 12 | — | — |
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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.80 | 0.97 | 27 | empty |
| 2 | 1110 | 0.79 | 0.81 | 83 | empty |
| 3 | 511 | 0.67 | 0.78 | 70 | empty |
| 4 | 96 | 0.51 | 0.82 | 26 | empty |
| 5 | 150 | 0.49 | 0.78 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2502 Ų buried · 15 hydrogen bonds · protein-protein
- A–T · 1109 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 864 Ų buried · 6 hydrogen bonds · protein-protein
- A–P · 645 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 497 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7OZV · SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with G · 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 7OZV · PDBe 7OZV · UniProt P0DTD1
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