Research workbench
A dual mechanism of action of at-527 against SARS-cov-2 polymerase
Analyse A dual mechanism of action of at-527 against SARS-cov-2 polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ED5
- Type
- protein + RNA
- Length
- 1,346 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; RNA (5'…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- AT9, MG, ZN
- Pockets
- 14 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 926 | 39% helix, 17% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 150 | 46% helix, 17% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 72 | 61% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 154 | 42% helix, 12% strand | P0DTD1 |
| I | RNA (5'- R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U*(AT9) )-3') | rna | 20 | — | — |
| J | RNA (5'- R(P*CP*CP*CP*CP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP *GP*C)-3') | rna | 24 | — | — |
Ligands and binding sites
- AT9 · [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · 3 copies · chains A, J, I
- MG · Magnesium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.83 | 0.85 | 76 | AT9 |
| 2 | 379 | 0.72 | 0.84 | 40 | MG, AT9 |
| 3 | 591 | 0.72 | 0.80 | 33 | empty |
| 4 | 427 | 0.65 | 0.78 | 52 | empty |
| 5 | 517 | 0.55 | 0.72 | 23 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2645 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1378 Ų buried · 2 hydrogen bonds · protein-protein
- A–J · 1078 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 911 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 895 Ų buried · 84 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7ED5 · A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase · 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 7ED5 · PDBe 7ED5 · UniProt P0DTD1
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