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Crystal structure of human Desmocollin-1 ectodomain
Analyse Crystal structure of human Desmocollin-1 ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IRY
- Type
- protein
- Length
- 1,078 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.095
- Source
- Homo sapiens
- Molecule
- Desmocollin-1
- UniProt
- Q08554
- Ligands
- MAN, NAG, BMA, CA
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · resolution 3.095 · 1 distinct chain · 1% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Desmocollin-1 | protein | 539 | 1% helix, 40% strand | Q08554 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 24 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.62 | 0.80 | 21 | empty |
| 2 | 88 | 0.32 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 760 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 6 disulfide (O-glycosylation, disulfide, N-glycosylation).
Compared structures
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 Q08554
- Elsewhere: RCSB PDB 5IRY · PDBe 5IRY · UniProt Q08554
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