MolNFT v1 · #16688 · protein
Prolyl oligopeptidase from porcine brain, D641N mutant with bound peptide ligand suc-gly-pro
1O6G · Prolyl endopeptidase: “Prolyl oligopeptidase from porcine brain, D641N mutant with bound peptide ligand suc-gly-pro”. X-ray diffraction, 7 pockets (best druggability 0.75). MolNFT v1 #16688 on GenesisL1: 3D structure, binding sites…
- PDB
- 1O6G
- Type
- protein
- Length
- 712 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
- Pockets
- 7 · best druggability 0.75
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 | 712 | 23% helix, 33% strand | P23687 |
Ligands and binding sites
- SIN · Succinic acid · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.75 | 0.79 | 72 | empty |
| 2 | 451 | 0.67 | 0.79 | 41 | empty |
| 3 | 244 | 0.53 | 0.77 | 33 | SIN |
| 4 | 88 | 0.39 | 0.76 | 17 | empty |
| 5 | 78 | 0.34 | 0.75 | 26 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 1O6G · Prolyl oligopeptidase from porcine brain, D641N mutant with bound peptide ligand… · 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 0.99
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 1O6G · PDBe 1O6G · UniProt P23687
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