MolNFT v1 · #119912 · protein
Three-dimensional reconstruction of human LRP6 ectodomain complexed with DKK1
5GJE · Low-density lipoprotein receptor-related protein 6: “Three-dimensional reconstruction of human LRP6 ectodomain complexed with DKK1”. Electron microscopy, 3 ligands (NAG, FUC, PO4), 10 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5GJE
- Type
- protein
- Length
- 1,293 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low-density lipoprotein receptor-related protein 6; Dickkopf-related protein 1
- UniProt
- O75581, O94907
- Ligands
- NAG, FUC, PO4
- Pockets
- 10 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low-density lipoprotein receptor-related protein 6 | protein | 611 | 2% helix, 43% strand | O75581 |
| B | Low-density lipoprotein receptor-related protein 6 | protein | 606 | 3% helix, 48% strand | O75581 |
| C | Dickkopf-related protein 1 | protein | 76 | 12% helix, 38% strand | O94907 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, C, B
- FUC · alpha-L-fucopyranose · sugar · chains B
- PO4 · Phosphate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.82 | 0.98 | 30 | empty |
| 2 | 813 | 0.80 | 0.83 | 66 | empty |
| 3 | 407 | 0.80 | 0.88 | 53 | empty |
| 4 | 1161 | 0.76 | 0.78 | 107 | empty |
| 5 | 260 | 0.75 | 0.88 | 48 | PO4 |
Interfaces
2 interfaces between chains.
- B–C · 1097 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 88 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5GJE · Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 · 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
- O94907 · AlphaFold monomer V2.0 prediction for dickkopf-related protein 1 (O94907) · a predicted model of the same protein · chain C 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
- Every structure of UniProt O94907
- Elsewhere: RCSB PDB 5GJE · PDBe 5GJE · UniProt O75581 · UniProt O94907
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