Research workbench
Prolyl oligopeptidase complexed with R-pro-(decarboxy-pro)-type inhibitors
Analyse Prolyl oligopeptidase complexed with R-pro-(decarboxy-pro)-type inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EQ8
- Type
- protein
- Length
- 709 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl endopeptidase
- EC
- 3.4.21.26
- UniProt
- P23687
- Ligands
- X98
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl endopeptidase (EC 3.4.21.26) | protein | 709 | 22% helix, 33% strand | P23687 |
Ligands and binding sites
- X98 · 1-{3-oxo-3-[(2S)-2-(pyrrolidin-1-ylcarbonyl)pyrrolidin-1-yl]propyl}-3-phenylquinoxalin-2(1H)-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.73 | 0.79 | 69 | empty |
| 2 | 550 | 0.65 | 0.76 | 47 | empty |
| 3 | 322 | 0.59 | 0.77 | 45 | X98 |
| 4 | 100 | 0.52 | 0.83 | 26 | empty |
| 5 | 73 | 0.35 | 0.76 | 15 | empty |
Compared structures
- 3EQ8 · Prolyl oligopeptidase complexed with R-Pro-(decarboxy-Pro)-Type inhibitors · 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 3EQ8 · PDBe 3EQ8 · UniProt P23687
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