MolNFT v1 · #155413 · protein
Crystal structure of LRP6 E1E2-sost complex
6L6R · Low-density lipoprotein receptor-related protein 6: “Crystal structure of LRP6 E1E2-sost complex”. X-ray diffraction, 3 ligands (NAG, FUC, MG), 11 pockets (best druggability 0.76). MolNFT v1 #155413 on GenesisL1: 3D structure…
- PDB
- 6L6R
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low-density lipoprotein receptor-related protein 6; Sclerostin
- UniProt
- O75581, Q9BQB4
- Ligands
- NAG, FUC, MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low-density lipoprotein receptor-related protein 6 | protein | 610 | 2% helix, 47% strand | O75581 |
| B | Low-density lipoprotein receptor-related protein 6 | protein | 610 | 2% helix, 47% strand | O75581 |
| C | Sclerostin | protein | 93 | 0% helix, 40% strand | Q9BQB4 |
| D | Sclerostin | protein | 91 | 0% helix, 42% strand | Q9BQB4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.76 | 0.88 | 44 | empty |
| 2 | 292 | 0.76 | 0.88 | 43 | empty |
| 3 | 74 | 0.74 | 0.98 | 31 | MG |
| 4 | 76 | 0.74 | 0.97 | 30 | MG |
| 5 | 591 | 0.70 | 0.79 | 77 | empty |
Interfaces
3 interfaces between chains.
- B–D · 983 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 964 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6L6R · Crystal structure of LRP6 E1E2-SOST complex · the same entry in another collection · chain D against D, 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
- Q9BQB4 · AlphaFold monomer V2.0 prediction for sclerostin (Q9BQB4) · a predicted model of the same protein · chain C against A, TM-score 0.77
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 Q9BQB4
- Elsewhere: RCSB PDB 6L6R · PDBe 6L6R · UniProt O75581 · UniProt Q9BQB4
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