Research workbench
Structure of LRP6 P3E3P4E4 in complex with vhh L-P2-B10
Analyse Structure of LRP6 P3E3P4E4 in complex with vhh L-P2-B10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H15
- Type
- protein
- Length
- 1,462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low-density lipoprotein receptor-related protein 6; Vhh L-P2-B10
- UniProt
- O75581
- Ligands
- NAG, BMA, MAN, CL
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Low-density lipoprotein receptor-related protein 6 | protein | 608 | 3% helix, 49% strand | O75581 |
| C, D | Vhh L-P2-B10 | protein | 123 | 10% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar
- CL · Chloride ion · ion · 7 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.83 | 0.96 | 34 | empty |
| 2 | 199 | 0.83 | 0.97 | 33 | empty |
| 3 | 659 | 0.80 | 0.85 | 58 | empty |
| 4 | 506 | 0.78 | 0.85 | 47 | empty |
| 5 | 1124 | 0.75 | 0.78 | 122 | CL |
Interfaces
4 interfaces between chains.
- D–B · 887 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 885 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 536 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 531 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6H15 · Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-B10 · 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 A 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
- Elsewhere: RCSB PDB 6H15 · PDBe 6H15 · UniProt O75581
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.