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Crystal structure of monomeric uncomplexed form of xenopus dishevelled PDZ domain
Analyse Crystal structure of monomeric uncomplexed form of xenopus dishevelled PDZ… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F0A
- Type
- protein
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Segment polarity protein dishevelled homolog dvl-2
- UniProt
- P51142
- Ligands
- CO, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Segment polarity protein dishevelled homolog dvl-2 | protein | 92 | 24% helix, 33% strand | P51142 |
| B | Segment polarity protein dishevelled homolog dvl-2 | protein | 88 | 23% helix, 33% strand | P51142 |
| C | Segment polarity protein dishevelled homolog dvl-2 | protein | 85 | 25% helix, 34% strand | P51142 |
| D | Segment polarity protein dishevelled homolog dvl-2 | protein | 87 | 18% helix, 38% strand | P51142 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.74 | 0.85 | 48 | empty |
| 2 | 197 | 0.66 | 0.85 | 40 | empty |
| 3 | 77 | 0.37 | 0.77 | 17 | empty |
| 4 | 60 | 0.29 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–D · 629 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 604 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 487 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 420 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 305 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2F0A · Crystal Structure of Monomeric Uncomplexed form of Xenopus dishevelled PDZ domain · the same entry in another collection · chain D against D, TM-score 1.00
- P51142 · 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 0.92
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 P51142
- Elsewhere: RCSB PDB 2F0A · PDBe 2F0A · UniProt P51142
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