Research workbench
Crystal structure of DSCAM1 isoform 7.44, N-terminal four ig domains
Analyse Crystal structure of DSCAM1 isoform 7.44, 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
- 4X83
- Type
- protein
- Length
- 1,558 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Down syndrome cell adhesion molecule, isoform 7.44
- Ligands
- NAG, CL
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Down syndrome cell adhesion molecule, isoform 7.44 | protein | 389 | 4% helix, 53% strand | — |
| D | Down syndrome cell adhesion molecule, isoform 7.44 | protein | 391 | 5% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.79 | 0.84 | 92 | empty |
| 2 | 545 | 0.74 | 0.82 | 67 | empty |
| 3 | 151 | 0.68 | 0.88 | 36 | empty |
| 4 | 271 | 0.67 | 0.83 | 38 | empty |
| 5 | 287 | 0.66 | 0.82 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1310 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1245 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 583 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 172 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 4X83 · Crystal structure of Dscam1 isoform 7.44, 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 4X83 · PDBe 4X83
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.