Research workbench
Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-4
Analyse Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AN1
- 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
- 2P8
- Pockets
- 8 · best druggability 0.71
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
- 2P8 · (2S)-N-benzyl-2-({(2S)-2-[(1R)-1,2-dihydroxyethyl]pyrrolidin-1-yl}carbonyl)pyrrolidine-1-carboxamide · 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.71 | 0.81 | 71 | empty |
| 2 | 320 | 0.65 | 0.80 | 39 | empty |
| 3 | 95 | 0.53 | 0.84 | 26 | empty |
| 4 | 153 | 0.52 | 0.79 | 27 | 2P8 |
| 5 | 86 | 0.38 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4AN1 · Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-4 · 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 4AN1 · PDBe 4AN1 · UniProt P23687
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