Research workbench
Inhibited dimeric pseudorabies virus protease PUL26N at 2 a resolution
Analyse Inhibited dimeric pseudorabies virus protease PUL26N at 2 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V08
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UL26
- EC
- 3.4.21.97
- UniProt
- Q83417
- Ligands
- DFP, MG, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UL26 (EC 3.4.21.97) | protein | 213 | 36% helix, 22% strand | Q83417 |
| B | UL26 (EC 3.4.21.97) | protein | 224 | 34% helix, 21% strand | Q83417 |
Ligands and binding sites
- DFP · Diisopropyl phosphonate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.76 | 0.97 | 22 | empty |
| 2 | 111 | 0.37 | 0.74 | 24 | DFP |
| 3 | 107 | 0.35 | 0.74 | 31 | DFP |
| 4 | 74 | 0.35 | 0.76 | 17 | empty |
| 5 | 85 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1311 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4V08 · Inhibited dimeric pseudorabies virus protease pUL26N at 2 A resolution · the same entry in another collection · chain B against B, 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 Q83417
- Elsewhere: RCSB PDB 4V08 · PDBe 4V08 · UniProt Q83417
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