Research workbench
Structure of human dipeptidyl peptidase 10 (dppy): a modulator of neuronal KV4 channels
Analyse Structure of human dipeptidyl peptidase 10 (dppy): a modulator of neuronal KV4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WJL
- Type
- protein
- Length
- 1,436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inactive dipeptidyl peptidase 10
- UniProt
- Q8N608
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inactive dipeptidyl peptidase 10 | protein | 717 | 14% helix, 33% strand | Q8N608 |
| B | Inactive dipeptidyl peptidase 10 | protein | 719 | 14% helix, 33% strand | Q8N608 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.79 | 0.81 | 100 | empty |
| 2 | 560 | 0.75 | 0.82 | 56 | empty |
| 3 | 142 | 0.67 | 0.88 | 33 | empty |
| 4 | 406 | 0.66 | 0.79 | 44 | empty |
| 5 | 420 | 0.65 | 0.78 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 1607 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 4WJL · Structure of human dipeptidyl peptidase 10 (DPPY): a modulator of neuronal Kv4 channels · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N608 · AlphaFold monomer V2.0 prediction for inactive dipeptidyl peptidase 10 (Q8N608) · a predicted model of the same protein · chain B 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 Q8N608
- Elsewhere: RCSB PDB 4WJL · PDBe 4WJL · UniProt Q8N608
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