MolNFT v1 · #109659 · protein
Crystal structure of DSCAM1 isoform 6.9, N-terminal four ig domains
4X9F · Down syndrome cell adhesion molecule isoform 6.9: “Crystal structure of DSCAM1 isoform 6.9, N-terminal four ig domains”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 11 pockets (best druggability 0.85). MolNFT v1 #109659 on…
- PDB
- 4X9F
- 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 6.9
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Down syndrome cell adhesion molecule isoform 6.9 | protein | 393 | 6% helix, 52% strand | — |
| B | Down syndrome cell adhesion molecule isoform 6.9 | protein | 390 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- SO4 · Sulfate ion · ion · 15 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.85 | 0.86 | 117 | GOL |
| 2 | 286 | 0.75 | 0.88 | 39 | empty |
| 3 | 68 | 0.58 | 0.89 | 26 | empty |
| 4 | 78 | 0.35 | 0.77 | 17 | empty |
| 5 | 60 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1821 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4X9F · Crystal structure of Dscam1 isoform 6.9, 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 4X9F · PDBe 4X9F
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