Research workbench
Pandda analysis group deposition SARS-cov-2 main protease fragment screen -- crystal structure of SARS-cov-2 main protease in complex with Z4444622180 (mpro-X2562)
Analyse Pandda analysis group deposition SARS-cov-2 main protease fragment screen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5RGU
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- UGD
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- UGD · N-(3-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyrimidin-5-yl)acetamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.52 | 0.77 | 27 | UGD |
| 2 | 90 | 0.48 | 0.82 | 20 | DMS |
| 3 | 51 | 0.32 | 0.77 | 17 | empty |
| 4 | 77 | 0.32 | 0.74 | 15 | empty |
Compared structures
- 5RGU · PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal… · 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 5RGU · PDBe 5RGU · UniProt P0DTD1
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