Research workbench
The crystal structure of COVID-19 main protease apo form at 2.2 ångström
Analyse The crystal structure of COVID-19 main protease apo form at 2.2 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E5X
- 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
- 15 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 24% 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 | 24% helix, 29% strand | P0DTD1 |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.79 | 0.81 | 98 | empty |
| 2 | 769 | 0.78 | 0.82 | 74 | empty |
| 3 | 649 | 0.78 | 0.84 | 68 | empty |
| 4 | 169 | 0.66 | 0.86 | 29 | empty |
| 5 | 363 | 0.58 | 0.76 | 53 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1515 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1462 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 656 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 331 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 72 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7E5X · THE CRYSTAL STRUCTURE OF COVID-19 MAIN PROTEASE apo form at 2.2 angstrom · 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 7E5X · PDBe 7E5X · UniProt P0DTD1
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