Research workbench
Prolyl oligopeptidase from porcine brain, mutant, complexed with peptide
Analyse Prolyl oligopeptidase from porcine brain, mutant, complexed with peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E8N
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl endopeptidase; Peptide inhibitor
- EC
- 3.4.21.26
- UniProt
- P23687
- Ligands
- BE2
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl endopeptidase (EC 3.4.21.26) | protein | 710 | 23% helix, 33% strand | P23687 |
| I | Peptide inhibitor | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.76 | 0.79 | 83 | empty |
| 2 | 889 | 0.74 | 0.78 | 83 | BE2, GOL |
| 3 | 96 | 0.51 | 0.82 | 26 | empty |
| 4 | 91 | 0.40 | 0.77 | 17 | empty |
| 5 | 54 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–I · 456 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1E8N · Prolyl oligopeptidase from porcine brain, mutant, complexed with peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P23687 · AlphaFold monomer V2.0 prediction for prolyl endopeptidase (P23687) · a predicted model of the same protein · 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 P23687
- Elsewhere: RCSB PDB 1E8N · PDBe 1E8N · UniProt P23687
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