Research workbench
Crystal structure of DSCAM1 isoform 8.4, N-terminal four ig domains
Analyse Crystal structure of DSCAM1 isoform 8.4, 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
- 4X9H
- Type
- protein
- Length
- 783 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Down syndrome cell adhesion molecule, isoform ap
- UniProt
- Q0E9L0
- Ligands
- NAG, BMA, MAN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Down syndrome cell adhesion molecule, isoform ap | protein | 391 | 4% helix, 50% strand | Q0E9L0 |
| B | Down syndrome cell adhesion molecule, isoform ap | protein | 392 | 3% helix, 47% strand | Q0E9L0 |
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 · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.83 | 0.86 | 103 | empty |
| 2 | 492 | 0.67 | 0.79 | 56 | empty |
| 3 | 392 | 0.64 | 0.79 | 55 | empty |
| 4 | 61 | 0.54 | 0.88 | 18 | empty |
| 5 | 129 | 0.38 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2337 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4X9H · Crystal structure of Dscam1 isoform 8.4, 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
- Every structure of UniProt Q0E9L0
- Elsewhere: RCSB PDB 4X9H · PDBe 4X9H · UniProt Q0E9L0
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