Research workbench
Crystal structure of prophenoloxidase activating factor-II from the beetle holotrichia diomphalia
Analyse Crystal structure of prophenoloxidase activating factor-II from the beetle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B9L
- Type
- protein
- Length
- 372 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prophenoloxidase activating factor
- Ligands
- NAG, FUC, CA, SO4
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prophenoloxidase activating factor | protein | 372 | 14% helix, 29% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.52 | 0.75 | 37 | empty |
| 2 | 130 | 0.48 | 0.79 | 33 | SO4 |
| 3 | 129 | 0.46 | 0.78 | 23 | empty |
| 4 | 57 | 0.42 | 0.82 | 16 | SO4 |
| 5 | 63 | 0.29 | 0.73 | 19 | empty |
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2B9L · Crystal structure of prophenoloxidase activating factor-II from the beetle Holotrichia… · 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
- Elsewhere: RCSB PDB 2B9L · PDBe 2B9L
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