Research workbench
Structure of LRP6 P3E3P4E4 in complex with vhh L-P2-D07
Analyse Structure of LRP6 P3E3P4E4 in complex with vhh L-P2-D07 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H16
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low-density lipoprotein receptor-related protein 6; Vhh L-P2-D07
- UniProt
- O75581
- Ligands
- NAG, BMA, MAN, CA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low-density lipoprotein receptor-related protein 6 | protein | 607 | 3% helix, 48% strand | O75581 |
| B | Vhh L-P2-D07 | protein | 119 | 5% helix, 57% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
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 | 178 | 0.82 | 0.97 | 32 | empty |
| 2 | 576 | 0.79 | 0.85 | 54 | CA |
| 3 | 348 | 0.63 | 0.79 | 42 | empty |
| 4 | 124 | 0.38 | 0.74 | 26 | empty |
| 5 | 79 | 0.37 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 839 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6H16 · Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-D07 · 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 0.98
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 6H16 · PDBe 6H16 · UniProt O75581
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