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Crystal structure of mg-132 covalently bound to the main protease (3CLPRO/MPRO) of SARS-cov-2 in absence of dtt.
Analyse Crystal structure of mg-132 covalently bound to the main protease (3CLPRO/MPRO)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BGP
- Type
- protein
- Length
- 606 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, NA, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 25% helix, 28% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 30% 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
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 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 | 0.76 | 0.78 | 84 | empty |
| 2 | 353 | 0.56 | 0.75 | 58 | EDO |
| 3 | 187 | 0.49 | 0.77 | 32 | ALD |
| 4 | 194 | 0.49 | 0.76 | 28 | ALD |
| 5 | 85 | 0.37 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1465 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7BGP · 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 7BGP · PDBe 7BGP · UniProt P0DTD1
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