Research workbench
Pandda analysis group deposition -- crystal structure of SARS-cov-2 nendou in complex with Z425449682
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
- 5SAD
- Type
- protein
- Length
- 696 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
- EJW
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 21% helix, 32% strand | P0DTD1 |
Ligands and binding sites
- EJW · (3-phenyl-1,2-oxazol-5-yl)methylazanium · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.58 | 0.80 | 26 | empty |
| 2 | 205 | 0.58 | 0.80 | 30 | empty |
| 3 | 122 | 0.42 | 0.76 | 17 | empty |
| 4 | 108 | 0.39 | 0.75 | 20 | empty |
| 5 | 79 | 0.31 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5SAD · 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 5SAD · PDBe 5SAD · UniProt P0DTD1
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