Research workbench
Co-crystal structure of SARS-cov-2 mpro C145A with substrate peptide 8/9
Analyse Co-crystal structure of SARS-cov-2 mpro C145A with substrate peptide 8/9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T9Y
- Type
- protein
- Length
- 625 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Nonstructural protein 8/9
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 302 | 25% helix, 28% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 25% helix, 29% strand | P0DTD1 |
| C | Nonstructural protein 8/9 | protein | 8 | 0% helix, 38% strand | — |
| D | Nonstructural protein 8/9 | protein | 10 | 0% helix, 40% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.76 | 0.80 | 83 | empty |
| 2 | 254 | 0.52 | 0.75 | 40 | empty |
| 3 | 157 | 0.44 | 0.75 | 28 | empty |
| 4 | 119 | 0.40 | 0.75 | 29 | empty |
| 5 | 75 | 0.37 | 0.77 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1513 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 819 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 740 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7T9Y · Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 8/9 · 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 7T9Y · PDBe 7T9Y · UniProt P0DTD1
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