Research workbench
Crystal structure of SARS-cov-2 nendou in complex with liza-7
Analyse Crystal structure of SARS-cov-2 nendou in complex with liza-7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N7U
- 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
- 0MI
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 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
- 0MI · 1-[(2~{R},4~{S},5~{R})-5-[[(azanylidene-$l^{4}-azanylidene)amino]methyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione · 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 | 265 | 0.61 | 0.80 | 33 | empty |
| 2 | 216 | 0.60 | 0.81 | 27 | empty |
| 3 | 130 | 0.41 | 0.75 | 22 | empty |
| 4 | 111 | 0.38 | 0.75 | 22 | empty |
| 5 | 61 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 611 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7N7U · Crystal Structure of SARS-CoV-2 NendoU in complex with LIZA-7 · 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 7N7U · PDBe 7N7U · UniProt P0DTD1
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