Research workbench
Crystal structure of LRP6-DKK1 complex
Analyse Crystal structure of LRP6-DKK1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S8V
- Type
- protein
- Length
- 1,277 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low-density lipoprotein receptor-related protein 6; Dickkopf-related protein 1
- UniProt
- O75581, O94907
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low-density lipoprotein receptor-related protein 6 | protein | 600 | 3% helix, 47% strand | O75581 |
| B | Low-density lipoprotein receptor-related protein 6 | protein | 604 | 3% helix, 48% strand | O75581 |
| X | Dickkopf-related protein 1 | protein | 73 | 10% helix, 32% strand | O94907 |
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.81 | 0.98 | 32 | empty |
| 2 | 149 | 0.81 | 0.97 | 29 | empty |
| 3 | 575 | 0.79 | 0.85 | 62 | empty |
| 4 | 606 | 0.78 | 0.84 | 57 | empty |
| 5 | 1072 | 0.75 | 0.78 | 95 | empty |
Interfaces
3 interfaces between chains.
- A–X · 1130 Ų buried · 11 hydrogen bonds · protein-protein
- B–X · 1037 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 187 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 3S8V · Crystal structure of LRP6-Dkk1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- O75581 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor-related protein 6… · a predicted model of the same protein · chain B against A, TM-score 0.95
- O94907 · AlphaFold monomer V2.0 prediction for dickkopf-related protein 1 (O94907) · a predicted model of the same protein · chain X against A, TM-score 0.95
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
- Every structure of UniProt O94907
- Elsewhere: RCSB PDB 3S8V · PDBe 3S8V · UniProt O75581 · UniProt O94907
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