Research workbench
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-100112
Analyse PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SAH
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.16
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Ligands
- ZQJ
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.16 · 1 distinct chain · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 22% helix, 32% strand | P0DTD1 |
Ligands and binding sites
- ZQJ · 2-methyl-5,6,7,8-tetrahydropyrido[4,3-c]pyridazin-3(2H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.59 | 0.80 | 27 | empty |
| 2 | 235 | 0.58 | 0.79 | 25 | empty |
| 3 | 134 | 0.42 | 0.75 | 20 | empty |
| 4 | 112 | 0.39 | 0.75 | 21 | empty |
| 5 | 84 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5SAH · Pandda analysis group deposition -- crystal structure of SARS-cov-2 nendou in complex… · 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 5SAH · PDBe 5SAH · UniProt P0DTD1
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