Research workbench
Structure of COVID-19 RNA-dependent RNA polymerase bound to favipiravir
Analyse Structure of COVID-19 RNA-dependent RNA polymerase bound to favipiravir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DFG
- Type
- protein + RNA
- Length
- 1,228 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(P*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3'); RNA (5'…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- POP, 1RP, MG, ZN
- Pockets
- 12 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | RNA (5'-R(P*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3') | rna | 12 | — | — |
| T | RNA (5'- R(P*CP*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*U)-3') | rna | 16 | — | — |
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 908 | 42% helix, 18% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 117 | 41% helix, 25% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 69 | 72% helix, 0% strand | P0DTD1 |
| G | Non-structural protein 8 | protein | 106 | 30% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A
- 1RP · 6-fluoro-3-oxo-4-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydropyrazine-2-carboxamide · ligand · chains P, T, A
- MG · Magnesium ion · metal · 4 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.80 | 0.97 | 28 | empty |
| 2 | 903 | 0.79 | 0.82 | 66 | 1RP, POP, MG |
| 3 | 525 | 0.68 | 0.78 | 62 | empty |
| 4 | 299 | 0.58 | 0.77 | 30 | POP, MG |
| 5 | 184 | 0.53 | 0.78 | 28 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2517 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 1301 Ų buried · 5 hydrogen bonds · protein-protein
- T–A · 1143 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 864 Ų buried · 6 hydrogen bonds · protein-protein
- P–A · 592 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7DFG · Structure of COVID-19 RNA-dependent RNA polymerase bound to favipiravir · the same entry in another collection · chain T against T, 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 7DFG · PDBe 7DFG · UniProt P0DTD1
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