Research workbench
Domain-swapped dimer of human DISHEVELLED2 dep domain: monoclinic crystal form crystallised from dimeric fraction
Analyse Domain-swapped dimer of human DISHEVELLED2 dep domain: monoclinic crystal form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SUY
- Type
- protein
- Length
- 378 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Segment polarity protein dishevelled homolog dvl-2
- UniProt
- O14641
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Segment polarity protein dishevelled homolog dvl-2 | protein | 95 | 35% helix, 21% strand | O14641 |
| B | Segment polarity protein dishevelled homolog dvl-2 | protein | 94 | 36% helix, 23% strand | O14641 |
| D | Segment polarity protein dishevelled homolog dvl-2 | protein | 94 | 35% helix, 21% strand | O14641 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.75 | 0.79 | 74 | empty |
| 2 | 72 | 0.31 | 0.74 | 22 | empty |
| 3 | 62 | 0.27 | 0.73 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2624 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2607 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 302 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 258 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 218 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5SUY · Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form… · the same entry in another collection · chain D against D, TM-score 1.00
- O14641 · AlphaFold monomer V2.0 prediction for segment polarity protein dishevelled homolog dvl-2… · a predicted model of the same protein · chain C against A, TM-score 0.69
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 O14641
- Elsewhere: RCSB PDB 5SUY · PDBe 5SUY · UniProt O14641
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