Research workbench
SARS-cov-2 NSP15 endoribonuclease pre-cleavage state
Analyse SARS-cov-2 NSP15 endoribonuclease pre-cleavage state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N33
- Type
- protein
- Length
- 2,076 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Ligands
- UFT
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 346 | 21% helix, 32% strand | P0DTD1 |
Ligands and binding sites
- UFT · 2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate) · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.85 | 0.90 | 129 | empty |
| 2 | 359 | 0.78 | 0.89 | 48 | empty |
| 3 | 235 | 0.75 | 0.89 | 45 | empty |
| 4 | 374 | 0.71 | 0.83 | 51 | empty |
| 5 | 444 | 0.69 | 0.80 | 51 | empty |
Interfaces
15 interfaces between chains.
- D–E · 1159 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1158 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1156 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1139 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1136 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7N33 · SARS-CoV-2 Nsp15 endoribonuclease pre-cleavage state · the same entry in another collection · chain B against B, 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 7N33 · PDBe 7N33 · UniProt P0DTD1
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