Research workbench
Crystal structure of Dscam1 isoform 4.44, N-terminal four Ig domains
Analyse Crystal structure of Dscam1 isoform 4.44, N-terminal four Ig domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X9B
- Type
- protein
- Length
- 775 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Drosophila melanogaster
- Molecule
- Down syndrome cell adhesion molecule, isoform 4.44
- Ligands
- NAG, BMA, MAN, NA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Down syndrome cell adhesion molecule, isoform 4.44 | protein | 392 | 5% helix, 52% strand | — |
| B | Down syndrome cell adhesion molecule, isoform 4.44 | protein | 383 | 5% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.80 | 0.82 | 115 | empty |
| 2 | 259 | 0.67 | 0.84 | 47 | empty |
| 3 | 91 | 0.64 | 0.90 | 27 | empty |
| 4 | 105 | 0.45 | 0.78 | 19 | empty |
| 5 | 100 | 0.43 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1603 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4X9B · Crystal structure of DSCAM1 isoform 4.44, N-terminal four ig domains · 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 4X9B · PDBe 4X9B
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