MolNFT v1 · #95741 · protein
Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme complexes and product complexes.
4IZJ · Yellowtail ascites virus (yav) VP4 protease: “Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme…”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.58).…
- PDB
- 4IZJ
- Type
- protein
- Length
- 1,014 residues
- Chains
- 5
- 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
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Yellowtail ascites virus (yav) VP4 protease (EC 3.4.21.115) | protein | 203 | 21% helix, 33% strand | P89521 |
| B | Yellowtail ascites virus (yav) VP4 protease (EC 3.4.21.115) | protein | 202 | 23% helix, 35% strand | P89521 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- BME · Beta-mercaptoethanol · additive · 6 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.58 | 0.80 | 44 | empty |
| 2 | 50 | 0.45 | 0.85 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 977 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 956 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 955 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 949 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified, 5 disulfide (oxidation, disulfide).
Compared structures
- 4IZJ · Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site… · 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 4IZJ · PDBe 4IZJ · UniProt P89521
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