Research workbench
SARS-cov-2 rdrp with molnupiravir/ nhc in the template strand base- paired with a
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
- 7OZU
- 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
- 9 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1AB | protein | 814 | 46% helix, 15% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 115 | 43% helix, 25% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 62 | 87% 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.81 | 0.82 | 85 | empty |
| 2 | 156 | 0.80 | 0.96 | 27 | empty |
| 3 | 408 | 0.67 | 0.80 | 52 | empty |
| 4 | 64 | 0.58 | 0.89 | 19 | empty |
| 5 | 207 | 0.53 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2452 Ų buried · 12 hydrogen bonds · protein-protein
- A–T · 1105 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 911 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 641 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–T · 499 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7OZU · SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with A · 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 7OZU · PDBe 7OZU · UniProt P0DTD1
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