Research workbench
Structure of X-prolyl dipeptidyl aminopeptidase from lactobacillus helveticus
Analyse Structure of X-prolyl dipeptidyl aminopeptidase from lactobacillus helveticus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NFF
- Type
- protein
- Length
- 794 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro dipeptidyl-peptidase
- EC
- 3.4.14.11
- UniProt
- Q59485
- Ligands
- CA, PO4
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-pro dipeptidyl-peptidase (EC 3.4.14.11) | protein | 794 | 29% helix, 26% strand | Q59485 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 17 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 | 275 | 0.61 | 0.79 | 28 | empty |
| 2 | 74 | 0.57 | 0.88 | 27 | EDO |
| 3 | 192 | 0.52 | 0.77 | 39 | EDO |
| 4 | 117 | 0.45 | 0.78 | 19 | PO4 |
| 5 | 112 | 0.40 | 0.76 | 22 | empty |
Compared structures
- 6NFF · Structure of X-prolyl dipeptidyl aminopeptidase from Lactobacillus helveticus · the same entry in another collection · chain A against A, TM-score 1.00
- Q59485 · AlphaFold monomer V2.0 prediction for xaa-pro dipeptidyl-peptidase (Q59485) · 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 Q59485
- Elsewhere: RCSB PDB 6NFF · PDBe 6NFF · UniProt Q59485
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