Research workbench
Crystal structure of gsk-3/AXIN complex bound to phosphorylated wnt receptor LRP6 C-motif
Analyse Crystal structure of gsk-3/AXIN complex bound to phosphorylated wnt receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NM5
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GSK3B protein; Axin-1; Phosphorylated wnt receptor LRP6 C-motif
- EC
- 2.7.11.26
- UniProt
- Q6FI27, O15169
- Ligands
- ADP, MG, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GSK3B protein (EC 2.7.11.26) | protein | 361 | 33% helix, 20% strand | Q6FI27 |
| B | Axin-1 | protein | 19 | 79% helix, 0% strand | O15169 |
| C | Phosphorylated wnt receptor LRP6 C-motif | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.66 | 0.78 | 44 | ADP, MG |
| 2 | 74 | 0.40 | 0.79 | 23 | empty |
| 3 | 52 | 0.31 | 0.76 | 13 | GOL |
| 4 | 68 | 0.31 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 713 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 480 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4NM5 · Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif · the same entry in another collection · chain A against A, TM-score 1.00
- O15169 · AlphaFold monomer V2.0 prediction for axin-1 (O15169) · a predicted model of the same protein · chain B against A, TM-score 0.67
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 Q6FI27
- Every structure of UniProt O15169
- Elsewhere: RCSB PDB 4NM5 · PDBe 4NM5 · UniProt Q6FI27 · UniProt O15169
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