Research workbench
Structure of the invertebrate ALK grd
Analyse Structure of the invertebrate ALK grd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LIR
- Type
- protein
- Length
- 683 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALK tyrosine kinase receptor homolog scd-2
- EC
- 2.7.10.1
- UniProt
- O76411
- Ligands
- NAG, FUC, MAN, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALK tyrosine kinase receptor homolog scd-2 (EC 2.7.10.1) | protein | 347 | 6% helix, 27% strand | O76411 |
| B | ALK tyrosine kinase receptor homolog scd-2 (EC 2.7.10.1) | protein | 336 | 6% helix, 25% strand | O76411 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.67 | 0.79 | 50 | empty |
| 2 | 483 | 0.61 | 0.75 | 70 | empty |
| 3 | 104 | 0.36 | 0.74 | 17 | SO4 |
| 4 | 73 | 0.34 | 0.76 | 17 | empty |
| 5 | 59 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1039 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 10 modified, 8 glycan (disulfide, engineered, 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 O76411
- Elsewhere: RCSB PDB 7LIR · PDBe 7LIR · UniProt O76411
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