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Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with PF00835231
Analyse Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8J3A
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.91
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase nsp5
- EC
- 3.4.22.69
- UniProt
- P0DTC1
- Ligands
- V2M
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.91 · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 282 | 24% helix, 32% strand | P0DTC1 |
| B | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 290 | 25% helix, 30% strand | P0DTC1 |
Ligands and binding sites
- V2M · N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.74 | 0.80 | 63 | empty |
| 2 | 111 | 0.45 | 0.79 | 26 | empty |
| 3 | 97 | 0.44 | 0.79 | 20 | empty |
| 4 | 109 | 0.39 | 0.75 | 22 | V2M |
| 5 | 127 | 0.38 | 0.74 | 20 | V2M |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 P0DTC1
- Elsewhere: RCSB PDB 8J3A · PDBe 8J3A · UniProt P0DTC1
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