Research workbench
complex structure of CoV 229E 3CL protease with EPDTC
Analyse complex structure of CoV 229E 3CL protease with EPDTC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZU2
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Human coronavirus
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P0C6U2
- Ligands
- DTZ
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.-) | protein | 300 | 25% helix, 29% strand | P0C6U2 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 301 | 25% helix, 29% strand | P0C6U2 |
Ligands and binding sites
- DTZ · zinc(II)hydrogensulfide · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.77 | 0.79 | 143 | empty |
| 2 | 886 | 0.76 | 0.79 | 91 | empty |
| 3 | 215 | 0.54 | 0.78 | 32 | DTZ |
| 4 | 197 | 0.49 | 0.76 | 29 | MPD, DTZ |
Interfaces
1 interface between chains.
- A–B · 1489 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2ZU2 · Complex structure of cov 229E 3CL protease with epdtc · 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 P0C6U2
- Elsewhere: RCSB PDB 2ZU2 · PDBe 2ZU2 · UniProt P0C6U2
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