Research workbench
Structure of prolyl endoprotease from Aspergillus niger CBS 109712
Analyse Structure of prolyl endoprotease from Aspergillus niger CBS 109712 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8B57
- Type
- protein
- Length
- 485 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.42
- Source
- Aspergillus niger
- Molecule
- Prolyl Endoprotease from Aspergillus niger CBS 109712
- Ligands
- NAG, MAN, BMA
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.42 · 1 distinct chain · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl Endoprotease from Aspergillus niger CBS 109712 | protein | 485 | 42% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
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 | 746 | 0.74 | 0.79 | 58 | PG4, 1PE |
| 2 | 52 | 0.24 | 0.72 | 17 | empty |
Modifications
Observed in the structure: 7 glycan, 3 disulfide (N-glycosylation, disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8B57 · PDBe 8B57
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