Research workbench
Co-crystal structure of SARS-cov-2 mpro C145A with substrate peptide 4/5
Analyse Co-crystal structure of SARS-cov-2 mpro C145A with substrate peptide 4/5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T70
- Type
- protein
- Length
- 634 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Nonstructural protein 4/5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 25% helix, 28% strand | P0DTD1 |
| C, D | Nonstructural protein 4/5 | protein | 12 | 0% helix, 42% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 18 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 14 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.77 | 0.79 | 94 | DMS, GOL |
| 2 | 327 | 0.52 | 0.73 | 41 | GOL, DMS |
| 3 | 159 | 0.44 | 0.75 | 28 | empty |
| 4 | 119 | 0.41 | 0.75 | 26 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 1598 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 866 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 827 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7T70 · Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 4/5 · 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 7T70 · PDBe 7T70 · UniProt P0DTD1
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