Research workbench
Sortilin-progranulin interaction with compound 17
Analyse Sortilin-progranulin interaction with compound 17 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X48
- Type
- protein
- Length
- 654 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin
- UniProt
- Q99523
- Ligands
- UP4, UNL, NAG, BMA, MAN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin | protein | 654 | 6% helix, 39% strand | Q99523 |
Ligands and binding sites
- UP4 · N-(3,5-dichlorobenzene-1-carbonyl)-5,5-dimethyl-L-norleucine · ligand · chains A
- UNL · Unknown ligand · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.65 | 0.77 | 58 | empty |
| 2 | 138 | 0.46 | 0.77 | 24 | UP4 |
| 3 | 136 | 0.43 | 0.76 | 24 | empty |
| 4 | 87 | 0.33 | 0.73 | 23 | UNL |
Modifications
Observed in the structure: 2 glycan (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 Q99523
- Elsewhere: RCSB PDB 6X48 · PDBe 6X48 · UniProt Q99523
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