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Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2
Analyse Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XDH
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.35 · 2 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 21% helix, 31% strand | P0DTD1 |
| B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 349 | 22% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- FMT · Formic acid · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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 | 240 | 0.59 | 0.80 | 30 | empty |
| 2 | 191 | 0.57 | 0.80 | 29 | empty |
| 3 | 62 | 0.34 | 0.77 | 14 | empty |
| 4 | 78 | 0.32 | 0.74 | 16 | empty |
| 5 | 70 | 0.32 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 600 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6XDH · Crystal structure of nendou (uridylate-specific endoribonuclease, NSP15) from… · 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 6XDH · PDBe 6XDH · UniProt P0DTD1
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