Research workbench
Crystal structure of the main protease of coronavirus HKU4
Analyse Crystal structure of the main protease of coronavirus HKU4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YNA
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69, 3.4.22.-
- UniProt
- P0C6T4
- Ligands
- NI
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69, 3.4.22.-) | protein | 306 | 25% helix, 28% strand | P0C6T4 |
| B | 3C-like proteinase (EC 3.4.22.69, 3.4.22.-) | protein | 302 | 25% helix, 30% strand | P0C6T4 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.78 | 0.80 | 62 | empty |
| 2 | 334 | 0.61 | 0.78 | 51 | GOL |
| 3 | 364 | 0.59 | 0.76 | 45 | GOL |
| 4 | 300 | 0.59 | 0.78 | 47 | GOL |
| 5 | 285 | 0.56 | 0.77 | 40 | NI, IMD |
Interfaces
1 interface between chains.
- A–B · 1368 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2YNA · Crystal structure of the main protease of coronavirus HKU4 · 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 P0C6T4
- Elsewhere: RCSB PDB 2YNA · PDBe 2YNA · UniProt P0C6T4
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