Research workbench
Crystal structure of dipeptidyl peptidase 11 (DPP11) from porphyromonas gingivalis
Analyse Crystal structure of dipeptidyl peptidase 11 (DPP11) from porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y01
- Type
- protein
- Length
- 1,398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase S46
- UniProt
- A0A076NW73
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidase S46 | protein | 699 | 51% helix, 16% strand | A0A076NW73 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.72 | 0.77 | 83 | empty |
| 2 | 627 | 0.67 | 0.76 | 55 | GOL |
| 3 | 260 | 0.56 | 0.77 | 27 | empty |
| 4 | 410 | 0.55 | 0.73 | 62 | empty |
| 5 | 132 | 0.39 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 811 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4Y01 · Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis · 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 A0A076NW73
- Elsewhere: RCSB PDB 4Y01 · PDBe 4Y01 · UniProt A0A076NW73
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