Research workbench
Cryo-EM structure of favipiravir bound to replicating polymerase complex of SARS-cov-2 in the pre-catalytic state.
Analyse Cryo-EM structure of favipiravir bound to replicating polymerase complex of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CTT
- Type
- protein + RNA
- Length
- 1,065 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…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- GE6, ZN, MG
- Pockets
- 9 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 826 | 41% helix, 14% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 114 | 35% helix, 24% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 63 | 79% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 28 | 86% helix, 0% strand | P0DTD1 |
| Q | Primer-RNA (5'- R(P*UP*UP*CP*UP*CP*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*A)-3') | rna | 16 | — | — |
| T | Template-RNA (5'- R(P*AP*CP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*GP*GP*AP*GP*AP*A)-3') | rna | 18 | — | — |
Ligands and binding sites
- GE6 · [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, Q, T
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.80 | 0.82 | 82 | MG, GE6 |
| 2 | 94 | 0.76 | 0.98 | 23 | empty |
| 3 | 432 | 0.65 | 0.78 | 54 | empty |
| 4 | 159 | 0.51 | 0.79 | 30 | empty |
| 5 | 75 | 0.34 | 0.76 | 15 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2456 Ų buried · 12 hydrogen bonds · protein-protein
- A–T · 1044 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 853 Ų buried · 5 hydrogen bonds · protein-protein
- Q–T · 737 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- C–D · 705 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7CTT · Cryo-EM structure of Favipiravir bound to replicating polymerase complex of SARS-CoV-2 in… · 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 7CTT · PDBe 7CTT · UniProt P0DTD1
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