Research workbench
SARS-cov-2 endoribonuclease NSP15 bound to dsrna
Analyse SARS-cov-2 endoribonuclease NSP15 bound to dsrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TQV
- Type
- protein + RNA
- Length
- 2,149 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease; RNA (33-mer)
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 21% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 21% helix, 29% strand | P0DTD1 |
| B, C, D, E, F | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 22% helix, 27% strand | P0DTD1 |
| G | RNA (33-mer) | rna | 33 | — | — |
| H | RNA (33-mer) | rna | 33 | — | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.87 | 0.90 | 117 | empty |
| 2 | 801 | 0.76 | 0.81 | 65 | empty |
| 3 | 652 | 0.70 | 0.78 | 69 | empty |
| 4 | 778 | 0.69 | 0.76 | 60 | empty |
| 5 | 478 | 0.68 | 0.79 | 50 | empty |
Interfaces
21 interfaces between chains.
- G–H · 1565 Ų buried · 158 hydrogen bonds · nucleic-nucleic
- A–C · 1322 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 1289 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1287 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1247 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7TQV · SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA · 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 7TQV · PDBe 7TQV · UniProt P0DTD1
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