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Structure of SARS cov-2 main protease shows simultaneous processing of its N- and C-terminii
Analyse Structure of SARS cov-2 main protease shows simultaneous processing of its N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LMC
- Type
- protein
- Length
- 1,235 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 4 peptide; 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | Non-structural protein 4 peptide | protein | 6 | 0% helix, 33% strand | P0DTD1 |
| A, B, C | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 28% strand | P0DTD1 |
| D | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 27% strand | P0DTD1 |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.80 | 0.83 | 90 | empty |
| 2 | 674 | 0.77 | 0.82 | 55 | empty |
| 3 | 771 | 0.76 | 0.81 | 70 | empty |
| 4 | 403 | 0.69 | 0.81 | 59 | empty |
| 5 | 608 | 0.67 | 0.76 | 94 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1490 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1489 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 694 Ų buried · 13 hydrogen bonds · protein-protein
- F–D · 535 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 528 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7LMC · Structure of SARS CoV-2 main protease shows simultaneous processing of its N- and… · the same entry in another collection · chain E against E, 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 7LMC · PDBe 7LMC · UniProt P0DTD1
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