Research workbench
Mouse SORCS2 ectodomain (sortilin related VPS10 domain containing receptor 2)
Analyse Mouse SORCS2 ectodomain (sortilin related VPS10 domain containing receptor 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FG9
- Type
- protein
- Length
- 1,833 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VPS10 domain-containing receptor SORCS2
- UniProt
- Q9EPR5
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VPS10 domain-containing receptor SORCS2 | protein | 915 | 5% helix, 40% strand | Q9EPR5 |
| B | VPS10 domain-containing receptor SORCS2 | protein | 918 | 5% helix, 40% strand | Q9EPR5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.73 | 0.94 | 25 | empty |
| 2 | 104 | 0.70 | 0.92 | 24 | empty |
| 3 | 759 | 0.70 | 0.77 | 62 | empty |
| 4 | 148 | 0.70 | 0.90 | 31 | empty |
| 5 | 361 | 0.66 | 0.80 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 3053 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 6FG9 · Mouse SORCS2 ectodomain (sortilin related VPS10 domain containing receptor 2) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9EPR5 · AlphaFold monomer V2.0 prediction for VPS10 domain-containing receptor SORCS2 (Q9EPR5) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 Q9EPR5
- Elsewhere: RCSB PDB 6FG9 · PDBe 6FG9 · UniProt Q9EPR5
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