MolNFT v2 · #133730 · protein
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000933940912
5RVC · Non-structural protein 3: “PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with…”. X-ray diffraction at 1, 1 ligand (W7V), 3 pockets (best druggability 0.66). MolNFT v2 #133730 on…
- PDB
- 5RVC
- Type
- protein
- Length
- 336 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- W7V
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · resolution 1 · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 167 | 40% helix, 19% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 169 | 42% helix, 19% strand | P0DTD1 |
Ligands and binding sites
- W7V · (1R,5R)-N-methyl-N-(1H-pyrazol-4-yl)bicyclo[3.1.0]hexane-1-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.66 | 0.78 | 36 | empty |
| 2 | 163 | 0.54 | 0.80 | 31 | empty |
| 3 | 133 | 0.52 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5RVC · Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in… · 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 5RVC · PDBe 5RVC · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.