MolNFT v1 · #179652 · protein
Human wls in complex with WNT8A
7KC4 · Protein wnt-8A: “Human wls in complex with WNT8A”. Electron microscopy, 6 ligands (DR9, PLM, Y01), 15 pockets (best druggability 0.83). MolNFT v1 #179652 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KC4
- Type
- protein
- Length
- 771 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein wnt-8A; Protein wntless homolog
- UniProt
- Q9H1J5, Q5T9L3
- Ligands
- DR9, PLM, Y01, NAG, MAN, BMA
- Pockets
- 15 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Protein wnt-8A | protein | 278 | 36% helix, 11% strand | Q9H1J5 |
| B | Protein wntless homolog | protein | 493 | 45% helix, 18% strand | Q5T9L3 |
Ligands and binding sites
- DR9 · 1-cis-9-octadecanoyl-2-cis-9-hexadecanoyl phosphatidyl glycerol · ligand · 3 copies · chains D, B
- PLM · Palmitic acid · ligand · chains D, B
- Y01 · Cholesterol hemisuccinate · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains D, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.83 | 0.84 | 69 | PLM, DR9 |
| 2 | 410 | 0.66 | 0.80 | 41 | empty |
| 3 | 354 | 0.65 | 0.79 | 39 | empty |
| 4 | 213 | 0.61 | 0.81 | 31 | empty |
| 5 | 340 | 0.57 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- D–B · 2549 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 2 glycan, 1 lipid (disulfide, N-glycosylation, palmitoylation).
Compared structures
- 7KC4 · Human WLS in complex with WNT8A · the same entry in another collection · chain D against D, TM-score 1.00
- Q5T9L3 · AlphaFold monomer V2.0 prediction for protein wntless homolog (Q5T9L3) · a predicted model of the same protein · chain B against A, TM-score 0.90
- Q9H1J5 · AlphaFold monomer V2.0 prediction for protein wnt-8A (Q9H1J5) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 Q9H1J5
- Every structure of UniProt Q5T9L3
- Elsewhere: RCSB PDB 7KC4 · PDBe 7KC4 · UniProt Q9H1J5 · UniProt Q5T9L3
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