Research workbench
Sorla VPS10P domain in ligand-free form
Analyse Sorla VPS10P domain in ligand-free form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSX
- Type
- protein
- Length
- 606 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin-related receptor
- UniProt
- Q92673
- Ligands
- NAG, PO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin-related receptor | protein | 606 | 5% helix, 43% strand | Q92673 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
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 | 63 | 0.73 | 0.98 | 22 | empty |
| 2 | 476 | 0.62 | 0.76 | 45 | PO4, EDO |
| 3 | 236 | 0.49 | 0.74 | 30 | empty |
| 4 | 128 | 0.45 | 0.77 | 28 | EDO |
| 5 | 126 | 0.45 | 0.77 | 26 | empty |
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, 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 Q92673
- Elsewhere: RCSB PDB 3WSX · PDBe 3WSX · UniProt Q92673
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