MolNFT v1 · #133650 · protein
Pandda analysis group deposition -- crystal structure of SARS-cov-2 nendou in complex with Z56900771
5S6Y · Uridylate-specific endoribonuclease: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 nendou in complex with Z56900771”. X-ray diffraction, 1 ligand (WUJ), 8 pockets (best druggability 0.58). MolNFT v1 #133650 on…
- PDB
- 5S6Y
- 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
- WUJ
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 21% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- WUJ · N-[(furan-2-yl)methyl]urea · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, 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 | 227 | 0.58 | 0.80 | 27 | empty |
| 2 | 207 | 0.58 | 0.80 | 27 | empty |
| 3 | 105 | 0.36 | 0.74 | 23 | empty |
| 4 | 87 | 0.36 | 0.75 | 17 | empty |
| 5 | 85 | 0.34 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 601 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5S6Y · 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 5S6Y · PDBe 5S6Y · UniProt P0DTD1
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