Research workbench
Structure of a human A-type Potassium Channel Accelerating factor DPPX, a member of the dipeptidyl aminopeptidase family
Analyse Structure of a human A-type Potassium Channel Accelerating factor DPPX, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XFD
- Type
- protein
- Length
- 2,892 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Homo sapiens
- Molecule
- Dipeptidyl aminopeptidase-like protein 6
- Ligands
- NAG, BMA, MAN, NDG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · resolution 3 · 1 distinct chain · 14% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dipeptidyl aminopeptidase-like protein 6 | protein | 723 | 14% helix, 31% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains B, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.76 | 0.79 | 115 | empty |
| 2 | 718 | 0.75 | 0.80 | 84 | empty |
| 3 | 646 | 0.75 | 0.81 | 82 | empty |
| 4 | 649 | 0.75 | 0.81 | 83 | empty |
| 5 | 522 | 0.67 | 0.78 | 39 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1676 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1665 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 16 disulfide (N-glycosylation, disulfide).
Compared structures
- 1XFD · Structure of a human a-type potassium channel accelerating factor dppx, a member of the… · 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
- Elsewhere: RCSB PDB 1XFD · PDBe 1XFD
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