Research workbench
The structure of the first ywtd beta propeller domain of LRP6 in complex with a Fab
Analyse The structure of the first ywtd beta propeller domain of LRP6 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SOB
- Type
- protein
- Length
- 740 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Low-density lipoprotein receptor-related protein 6; Antibody heavy…
- UniProt
- O75581
- Ligands
- CA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody light chain | protein | 213 | 6% helix, 52% strand | — |
| B | Low-density lipoprotein receptor-related protein 6 | protein | 305 | 5% helix, 47% strand | O75581 |
| H | Antibody heavy chain | protein | 222 | 8% helix, 50% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.77 | 0.89 | 42 | empty |
| 2 | 92 | 0.76 | 0.97 | 30 | empty |
| 3 | 493 | 0.59 | 0.74 | 51 | empty |
| 4 | 186 | 0.44 | 0.73 | 30 | empty |
| 5 | 92 | 0.34 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1760 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 687 Ų buried · 13 hydrogen bonds · protein-protein
- L–B · 205 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 3SOB · The structure of the first YWTD beta propeller domain of LRP6 in complex with a FAB · the same entry in another collection · chain L against L, 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 0.99
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 3SOB · PDBe 3SOB · UniProt O75581
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