MolNFT v1 · #183144 · protein
Crystal structure of mg-132 covalently bound to the main protease (3CLPRO/MPRO) of SARS-cov-2 in spacegroup P1 in absence of dtt.
7NG6 · 3C-like proteinase: “Crystal structure of mg-132 covalently bound to the main protease (3CLPRO/MPRO) of SARS-cov-2 in spacegroup…”. X-ray diffraction, 2 ligands (ALD, CL), 7 pockets (best druggability 0.77). MolNFT v1 #183144 on…
- PDB
- 7NG6
- Type
- protein
- Length
- 607 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
- ALD, CL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 302 | 25% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- ALD · N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.77 | 0.79 | 88 | CL |
| 2 | 171 | 0.53 | 0.79 | 26 | ALD |
| 3 | 191 | 0.52 | 0.78 | 30 | ALD |
| 4 | 170 | 0.44 | 0.74 | 25 | empty |
| 5 | 155 | 0.43 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1535 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7NG6 · Crystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of… · 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 7NG6 · PDBe 7NG6 · UniProt P0DTD1
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