MolNFT v1 · #133649 · protein
Pandda analysis group deposition -- crystal structure of SARS-cov-2 nendou in complex with Z2889976755
5S6X · Uridylate-specific endoribonuclease: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 nendou in complex with Z2889976755”. X-ray diffraction, 1 ligand (WUG), 8 pockets (best druggability 0.59). MolNFT v1 #133649…
- PDB
- 5S6X
- 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
- WUG
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 20% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- WUG · 1-(2,4-dimethyl-1H-imidazol-5-yl)methanamine · 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 | 217 | 0.59 | 0.80 | 27 | empty |
| 2 | 238 | 0.59 | 0.79 | 28 | empty |
| 3 | 125 | 0.41 | 0.75 | 21 | empty |
| 4 | 123 | 0.39 | 0.74 | 21 | empty |
| 5 | 83 | 0.31 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 595 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5S6X · 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 5S6X · PDBe 5S6X · UniProt P0DTD1
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