Research workbench
Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-3
Analyse Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AN0
- Type
- protein
- Length
- 710 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
- 2P6
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 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 |
Ligands and binding sites
- 2P6 · (2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.73 | 0.79 | 69 | empty |
| 2 | 480 | 0.67 | 0.79 | 45 | GOL |
| 3 | 342 | 0.59 | 0.77 | 48 | 2P6 |
| 4 | 92 | 0.50 | 0.83 | 25 | empty |
| 5 | 101 | 0.41 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4AN0 · Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-3 · 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 4AN0 · PDBe 4AN0 · UniProt P23687
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