Research workbench
SARS-CoV2 major protease in complex with a covalent inhibitor SLL12.
Analyse SARS-CoV2 major protease in complex with a covalent inhibitor SLL12. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9EOR
- Type
- protein
- Length
- 1,851 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Severe acute respiratory syndrome coronavirus 2; SYNTHETIC CONSTRUCT
- Molecule
- 3C-like proteinase nsp5; Inhibitor SLL12
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- K
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.25 · 3 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 306 | 26% helix, 29% strand | P0DTD1 |
| C, E, F | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 305 | 26% helix, 30% strand | P0DTD1 |
| G, H, I, J, K, L | Inhibitor SLL12 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 7 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.77 | 0.81 | 79 | empty |
| 2 | 1058 | 0.76 | 0.79 | 89 | empty |
| 3 | 1106 | 0.76 | 0.79 | 88 | empty |
| 4 | 475 | 0.65 | 0.78 | 43 | empty |
| 5 | 630 | 0.63 | 0.74 | 64 | empty |
Interfaces
24 interfaces between chains.
- C–D · 1673 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 1665 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 1569 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 617 Ų buried · 11 hydrogen bonds · protein-protein
- D–J · 439 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (nonstandard).
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 9EOR · PDBe 9EOR · UniProt P0DTD1
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