Research workbench
APPEP_WT+PP closed state
Analyse APPEP_WT+PP closed state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IVM
- Type
- protein
- Length
- 682 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl endopeptidase
- UniProt
- Q9X6R4
- Ligands
- ZPR
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl endopeptidase | protein | 682 | 22% helix, 34% strand | Q9X6R4 |
Ligands and binding sites
- ZPR · N-benzyloxycarbonyl-L-prolyl-L-prolinal · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.69 | 0.83 | 35 | ZPR |
| 2 | 298 | 0.61 | 0.79 | 36 | empty |
| 3 | 161 | 0.52 | 0.79 | 36 | empty |
| 4 | 73 | 0.41 | 0.79 | 19 | empty |
| 5 | 67 | 0.34 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 8 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 3IVM · apPEP_WT+PP closed state · the same entry in another collection · 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 Q9X6R4
- Elsewhere: RCSB PDB 3IVM · PDBe 3IVM · UniProt Q9X6R4
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