Research workbench
SARS-cov-2 NSP15 endoribonuclease post-cleavage state
Analyse SARS-cov-2 NSP15 endoribonuclease post-cleavage state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N06
- Type
- protein + RNA
- Length
- 2,091 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease; RNA (5'-R(*AP*UP*A)-3')
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 21% helix, 31% strand | P0DTD1 |
| G, H, I | RNA (5'-R(*AP*UP*A)-3') | rna | 2 | — | — |
| J, K, L | RNA (5'-R(*AP*UP*A)-3') | rna | 1 | — | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.84 | 0.89 | 106 | empty |
| 2 | 194 | 0.73 | 0.89 | 50 | empty |
| 3 | 442 | 0.65 | 0.78 | 42 | empty |
| 4 | 340 | 0.65 | 0.80 | 40 | empty |
| 5 | 452 | 0.65 | 0.78 | 46 | empty |
Interfaces
18 interfaces between chains.
- D–E · 1154 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1153 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 1147 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1115 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1115 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7N06 · SARS-CoV-2 Nsp15 endoribonuclease post-cleavage state · 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 7N06 · PDBe 7N06 · UniProt P0DTD1
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