MolNFT v1 · #111349 · protein
HKU4 3CLPRO unbound structure
4YO9 · 3C-like proteinase: “HKU4 3CLPRO unbound structure”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.76). MolNFT v1 #111349 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YO9
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P0C6W3
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.-) | protein | 306 | 22% helix, 29% strand | P0C6W3 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 301 | 25% helix, 28% strand | P0C6W3 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- ACT · Acetate ion · additive · 4 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
- SIN · Succinic acid · additive · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.76 | 0.79 | 69 | ACT |
| 2 | 600 | 0.67 | 0.77 | 92 | SIN |
| 3 | 330 | 0.59 | 0.77 | 48 | IPA |
| 4 | 209 | 0.54 | 0.78 | 27 | ZN |
| 5 | 232 | 0.52 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1314 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4YO9 · HKU4 3CLpro unbound structure · 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 P0C6W3
- Elsewhere: RCSB PDB 4YO9 · PDBe 4YO9 · UniProt P0C6W3
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