Research workbench
The siah E3 ubiquitin ligases promote wnt/ beta-catenin signaling through mediating wnt-induced axin degradation
Analyse The siah E3 ubiquitin ligases promote wnt/ beta-catenin signaling through… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WZZ
- Type
- protein
- Length
- 801 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase SIAH1; Axin-1
- EC
- 6.3.2.-
- UniProt
- Q8IUQ4, O15169
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | E3 ubiquitin-protein ligase SIAH1 (EC 6.3.2.-) | protein | 190 | 21% helix, 42% strand | Q8IUQ4 |
| E, H | Axin-1 | protein | 11 | 0% helix, 45% strand | O15169 |
| F | Axin-1 | protein | 9 | 0% helix, 44% strand | O15169 |
| G | Axin-1 | protein | 10 | 0% helix, 40% strand | O15169 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.71 | 0.75 | 92 | empty |
| 2 | 334 | 0.58 | 0.76 | 42 | empty |
| 3 | 163 | 0.48 | 0.77 | 22 | empty |
| 4 | 82 | 0.40 | 0.78 | 17 | empty |
| 5 | 99 | 0.35 | 0.74 | 23 | empty |
Interfaces
7 interfaces between chains.
- B–D · 1069 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 702 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 680 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 656 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 655 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5WZZ · The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8IUQ4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase SIAH1 (Q8IUQ4) · a predicted model of the same protein · chain A against A, TM-score 0.95
- O15169 · AlphaFold monomer V2.0 prediction for axin-1 (O15169) · a predicted model of the same protein · chain H against A, TM-score 0.43
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 Q8IUQ4
- Every structure of UniProt O15169
- Elsewhere: RCSB PDB 5WZZ · PDBe 5WZZ · UniProt Q8IUQ4 · UniProt O15169
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