MolNFT v1 · #95742 · protein
Crystal structure of yellowtail ascites virus VP4 protease active site mutant (K674A) reveals both an acyl-enzyme complex and an empty active site
4IZK · Yellowtail ascites virus (yav) VP4 protease: “Crystal structure of yellowtail ascites virus VP4 protease active site mutant (K674A) reveals both an…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.62). MolNFT v1…
- PDB
- 4IZK
- Type
- protein
- Length
- 405 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yellowtail ascites virus (yav) VP4 protease
- EC
- 3.4.21.115
- UniProt
- P89521
- Ligands
- MG
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yellowtail ascites virus (yav) VP4 protease (EC 3.4.21.115) | protein | 202 | 20% helix, 36% strand | P89521 |
| B | Yellowtail ascites virus (yav) VP4 protease (EC 3.4.21.115) | protein | 203 | 21% helix, 34% strand | P89521 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.62 | 0.81 | 46 | MG |
| 2 | 66 | 0.43 | 0.81 | 23 | empty |
| 3 | 62 | 0.39 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 990 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent, 1 modified (disulfide, additive adduct, oxidation).
Compared structures
- 4IZK · Crystal structure of yellowtail ascites virus VP4 protease active site mutant (K674A)… · 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 P89521
- Elsewhere: RCSB PDB 4IZK · PDBe 4IZK · UniProt P89521
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