Research workbench
Crystal structure of VP4 protease from infectious pancreatic necrosis virus (ipnv) in space group P1
Analyse Crystal structure of VP4 protease from infectious pancreatic necrosis virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PNL
- Type
- protein
- Length
- 2,030 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease VP4
- UniProt
- Q703G9
- Ligands
- GAI
- Pockets
- 14 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Protease VP4 | protein | 203 | 21% helix, 35% strand | Q703G9 |
Ligands and binding sites
- GAI · Guanidine · ligand · 17 copies · chains A, B, H, C, D, E, F, G, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.61 | 0.81 | 40 | GAI |
| 2 | 118 | 0.60 | 0.86 | 26 | GAI |
| 3 | 117 | 0.60 | 0.86 | 30 | GAI |
| 4 | 93 | 0.60 | 0.88 | 32 | GAI |
| 5 | 217 | 0.59 | 0.80 | 47 | GAI |
Interfaces
10 interfaces between chains.
- H–I · 1078 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1047 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1026 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1025 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1021 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 2PNL · Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in… · 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 Q703G9
- Elsewhere: RCSB PDB 2PNL · PDBe 2PNL · UniProt Q703G9
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