Research workbench
The crystal structure of 3CL mainpro of SARS-cov-2 with C145S mutation
Analyse The crystal structure of 3CL mainpro of SARS-cov-2 with C145S mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XOA
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.82 | 0.83 | 116 | empty |
| 2 | 993 | 0.77 | 0.79 | 84 | EDO |
| 3 | 455 | 0.76 | 0.85 | 42 | EDO |
| 4 | 593 | 0.75 | 0.82 | 63 | empty |
| 5 | 455 | 0.61 | 0.75 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1527 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1494 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 565 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 476 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6XOA · The crystal structure of 3CL MainPro of SARS-CoV-2 with C145S mutation · 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 6XOA · PDBe 6XOA · UniProt P0DTD1
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