Research workbench
Sorla VPS10P domain in complex with its own propeptide fragment
Analyse Sorla VPS10P domain in complex with its own propeptide fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSY
- Type
- protein
- Length
- 673 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin-related receptor; Peptide from sortilin-related receptor
- UniProt
- Q92673
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin-related receptor | protein | 662 | 6% helix, 42% strand | Q92673 |
| C | Peptide from sortilin-related receptor | protein | 11 | 0% helix, 36% strand | Q92673 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.68 | 0.97 | 15 | empty |
| 2 | 585 | 0.65 | 0.75 | 53 | empty |
| 3 | 322 | 0.53 | 0.74 | 46 | empty |
| 4 | 94 | 0.40 | 0.78 | 19 | empty |
| 5 | 88 | 0.38 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 857 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3WSY · SorLA Vps10p domain in complex with its own propeptide fragment · the same entry in another collection · chain A against A, TM-score 1.00
- Q92673 · AlphaFold monomer V2.0 prediction for sortilin-related receptor (Q92673) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 3WSY · PDBe 3WSY · UniProt Q92673
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