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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5265428226
Analyse PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SRJ
- Type
- protein
- Length
- 336 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.05
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- R9L
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.05 · 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
- R9L · 3-{[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]methyl}-1lambda~6~-thietane-1,1-dione · 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 | 457 | 0.67 | 0.79 | 35 | empty |
| 2 | 148 | 0.53 | 0.80 | 24 | empty |
| 3 | 158 | 0.52 | 0.79 | 32 | R9L |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5SRJ · 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 5SRJ · PDBe 5SRJ · UniProt P0DTD1
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