Research workbench
Sorla VPS10P domain in complex with abeta-derived peptide
Analyse Sorla VPS10P domain in complex with abeta-derived peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WSZ
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin-related receptor; 10-mer peptide
- UniProt
- Q92673
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin-related receptor | protein | 561 | 4% helix, 42% strand | Q92673 |
| C | 10-mer peptide | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.59 | 0.75 | 45 | empty |
| 2 | 139 | 0.54 | 0.81 | 22 | empty |
| 3 | 98 | 0.42 | 0.77 | 19 | empty |
| 4 | 113 | 0.41 | 0.76 | 25 | empty |
| 5 | 80 | 0.39 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–C · 446 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 3 disulfide (N-glycosylation, disulfide).
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 3WSZ · PDBe 3WSZ · UniProt Q92673
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