MolNFT v1 · #182390 · protein
SARS coronavirus-2 main protease 3CL-pro binding ascorbate
7MPB · 3C-like proteinase: “SARS coronavirus-2 main protease 3CL-pro binding ascorbate”. X-ray diffraction, 1 ligand (ASC), 5 pockets (best druggability 0.76). MolNFT v1 #182390 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MPB
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- ASC
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 303 | 26% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 310 | 26% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- ASC · Ascorbic acid · ligand · 2 copies · chains A, B
- ETF · Trifluoroethanol · additive · 2 copies · chains A, B
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 | 873 | 0.76 | 0.80 | 73 | empty |
| 2 | 583 | 0.63 | 0.75 | 72 | empty |
| 3 | 212 | 0.48 | 0.75 | 28 | ASC, ETF |
| 4 | 158 | 0.47 | 0.77 | 21 | ASC, ETF |
| 5 | 171 | 0.45 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1732 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7MPB · SARS Coronavirus-2 Main Protease 3CL-pro binding Ascorbate · 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 7MPB · PDBe 7MPB · UniProt P0DTD1
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