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Crystal structure of human DISHEVELLED1 PDZ domain homotrimer
Analyse Crystal structure of human DISHEVELLED1 PDZ domain homotrimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LCA
- Type
- protein
- Length
- 722 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Segment polarity protein dishevelled homolog dvl-1
- UniProt
- O14640
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Segment polarity protein dishevelled homolog dvl-1 | protein | 86 | 21% helix, 35% strand | O14640 |
| B | Segment polarity protein dishevelled homolog dvl-1 | protein | 90 | 19% helix, 39% strand | O14640 |
| C, D, E, F, G, H | Segment polarity protein dishevelled homolog dvl-1 | protein | 91 | 20% helix, 38% strand | O14640 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.62 | 0.76 | 43 | SO4 |
| 2 | 288 | 0.57 | 0.77 | 31 | empty |
| 3 | 298 | 0.56 | 0.76 | 38 | empty |
| 4 | 184 | 0.53 | 0.79 | 33 | empty |
| 5 | 209 | 0.44 | 0.73 | 39 | empty |
Interfaces
10 interfaces between chains.
- A–C · 703 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 683 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 584 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 545 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 538 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6LCA · Crystal structure of human Dishevelled1 PDZ domain homotrimer · the same entry in another collection · chain H against H, TM-score 1.00
- O14640 · AlphaFold monomer V2.0 prediction for segment polarity protein dishevelled homolog dvl-1… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O14640
- Elsewhere: RCSB PDB 6LCA · PDBe 6LCA · UniProt O14640
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