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Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.18
Analyse Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DVL
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Low-density lipoprotein receptor-related protein 6; E3.18 Disulfide constrained peptide
- UniProt
- O75581
- Ligands
- NAG, MAN, FUC, BMA, CA
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low-density lipoprotein receptor-related protein 6 | protein | 610 | 3% helix, 49% strand | O75581 |
| B | E3.18 Disulfide constrained peptide | protein | 14 | 0% helix, 57% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.81 | 0.85 | 64 | CA, EDO |
| 2 | 239 | 0.79 | 0.92 | 48 | CA |
| 3 | 716 | 0.69 | 0.76 | 77 | EDO |
| 4 | 127 | 0.41 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 565 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan, 1 modified (disulfide, N-glycosylation, oxidation).
Compared structures
- O75581 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor-related protein 6… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O75581
- Elsewhere: RCSB PDB 8DVL · PDBe 8DVL · UniProt O75581
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