MolNFT v1 · #176225 · protein + RNA
Structure of COVID-19 RNA-dependent RNA polymerase bound to ribavirin
7DFH · RNA-directed RNA polymeras: “Structure of COVID-19 RNA-dependent RNA polymerase bound to ribavirin”. Electron microscopy, 4 ligands (POP, RVP, MG), 10 pockets (best druggability 0.80). MolNFT v1 #176225 on GenesisL1: 3D structure…
- PDB
- 7DFH
- Type
- protein + RNA
- Length
- 1,211 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymeras; Non-structural protein 8; Non-structural protein 7; RNA…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- POP, RVP, MG, ZN
- Pockets
- 10 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymeras (EC 2.7.7.48) | protein | 908 | 40% helix, 18% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 114 | 38% helix, 27% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 63 | 78% helix, 0% strand | P0DTD1 |
| G | Non-structural protein 8 | protein | 106 | 33% helix, 27% strand | P0DTD1 |
| P | RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*G*(LIG))-3') | rna | 8 | — | — |
| T | RNA (5'-R(P*CP*CP*CP*CP*CP*AP*CP*AP*UP*AP*GP*C)-3') | rna | 12 | — | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A
- RVP · Ribavirin monophosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 3 copies · chains A, P
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.80 | 0.82 | 72 | MG, POP, RVP |
| 2 | 139 | 0.79 | 0.97 | 27 | empty |
| 3 | 452 | 0.67 | 0.79 | 54 | empty |
| 4 | 258 | 0.65 | 0.82 | 38 | MG, POP |
| 5 | 255 | 0.54 | 0.77 | 43 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2381 Ų buried · 16 hydrogen bonds · protein-protein
- A–T · 1098 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–G · 1037 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 887 Ų buried · 9 hydrogen bonds · protein-protein
- A–P · 673 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7DFH · Structure of COVID-19 RNA-dependent RNA polymerase bound to ribavirin · the same entry in another collection · chain B against B, 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 7DFH · PDBe 7DFH · UniProt P0DTD1
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