MolNFT v1 · #188103 · protein
Co-crystal structure of SARS-cov-2 mpro C145A with substrate peptide 15/16
7TC4 · 3C-like proteinase: “Co-crystal structure of SARS-cov-2 mpro C145A with substrate peptide 15/16”. X-ray diffraction, 5 pockets (best druggability 0.77). MolNFT v1 #188103 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TC4
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Nonstructural protein 15/16
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
| C, D | Nonstructural protein 15/16 | protein | 9 | 0% helix, 33% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.77 | 0.79 | 89 | empty |
| 2 | 313 | 0.54 | 0.75 | 46 | empty |
| 3 | 164 | 0.44 | 0.75 | 29 | empty |
| 4 | 94 | 0.40 | 0.77 | 19 | empty |
| 5 | 100 | 0.35 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1632 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 786 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 774 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7TC4 · Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 15/16 · 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 7TC4 · PDBe 7TC4 · UniProt P0DTD1
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