Research workbench
Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with potential repurposing drug tipiracil
Analyse Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WXC
- Type
- protein
- Length
- 695 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Ligands
- CMU, PO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 22% helix, 31% strand | P0DTD1 |
| B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 22% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- CMU · 5-chloro-6-(1-(2-iminopyrrolidinyl) methyl) uracil · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.58 | 0.80 | 25 | empty |
| 2 | 237 | 0.58 | 0.79 | 34 | empty |
| 3 | 131 | 0.40 | 0.74 | 18 | empty |
| 4 | 133 | 0.39 | 0.73 | 22 | EDO |
| 5 | 93 | 0.34 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WXC · Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with potential… · 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 6WXC · PDBe 6WXC · UniProt P0DTD1
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