MolNFT v1 · #142859 · protein
Wnt signaling complex
6AHY · Frizzled-8: “Wnt signaling complex”. X-ray diffraction, 3 ligands (PAM, NAG, CL), 18 pockets (best druggability 0.81). MolNFT v1 #142859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AHY
- Type
- protein
- Length
- 1,251 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Frizzled-8; Proto-oncogene wnt-3
- UniProt
- Q61091, P56703
- Ligands
- PAM, NAG, CL
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Frizzled-8 | protein | 120 | 43% helix, 6% strand | Q61091 |
| B | Proto-oncogene wnt-3 | protein | 313 | 33% helix, 23% strand | P56703 |
| C | Frizzled-8 | protein | 122 | 43% helix, 5% strand | Q61091 |
| D | Proto-oncogene wnt-3 | protein | 309 | 35% helix, 22% strand | P56703 |
| E | Frizzled-8 | protein | 112 | 46% helix, 4% strand | Q61091 |
| F | Proto-oncogene wnt-3 | protein | 275 | 40% helix, 13% strand | P56703 |
Ligands and binding sites
- PAM · Palmitoleic acid · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, D, A, C, E, F
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.81 | 0.83 | 80 | empty |
| 2 | 378 | 0.70 | 0.83 | 53 | empty |
| 3 | 323 | 0.63 | 0.79 | 29 | empty |
| 4 | 161 | 0.49 | 0.77 | 19 | empty |
| 5 | 58 | 0.45 | 0.83 | 13 | empty |
Interfaces
6 interfaces between chains.
- B–F · 909 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 779 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 748 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 696 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 319 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 65 modified, 46 disulfide, 8 glycan, 2 covalent (methylation, disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6AHY · Wnt signaling complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q61091 · AlphaFold monomer V2.0 prediction for frizzled-8 (Q61091) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P56703 · AlphaFold monomer V2.0 prediction for proto-oncogene wnt-3 (P56703) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 Q61091
- Every structure of UniProt P56703
- Elsewhere: RCSB PDB 6AHY · PDBe 6AHY · UniProt Q61091 · UniProt P56703
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