Research workbench
Pandda analysis group deposition of ground-state model of SARS-cov-2 main protease screened against dsi poised (enamine), fraglites and peplites (newcastle university), mini frags (astex), york 3D (york university), electrophile cysteine covalent (weizman institute) fragment libraries
Analyse Pandda analysis group deposition of ground-state model of SARS-cov-2 main… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5R8T
- 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
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- DMS · Dimethyl sulfoxide · additive · 3 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.50 | 0.76 | 26 | empty |
| 2 | 87 | 0.47 | 0.81 | 16 | DMS |
| 3 | 59 | 0.32 | 0.76 | 16 | empty |
| 4 | 80 | 0.32 | 0.74 | 15 | empty |
Compared structures
- 5R8T · PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease… · 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 5R8T · PDBe 5R8T · UniProt P0DTD1
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