Research workbench
Crystal structure of the dhr-2 domain of DOCK8 in complex with CDC42 (T17N mutant)
Analyse Crystal structure of the dhr-2 domain of DOCK8 in complex with CDC42 (T17N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VHL
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dedicator of cytokinesis protein 8; Cell division control protein 42 homolog
- UniProt
- Q8C147, P60953
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dedicator of cytokinesis protein 8 | protein | 264 | 50% helix, 24% strand | Q8C147 |
| B | Cell division control protein 42 homolog | protein | 178 | 42% helix, 22% strand | P60953 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
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 | 690 | 0.70 | 0.77 | 52 | empty |
| 2 | 165 | 0.60 | 0.83 | 27 | empty |
| 3 | 69 | 0.45 | 0.82 | 23 | empty |
| 4 | 78 | 0.31 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2244 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3VHL · Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant) · the same entry in another collection · chain A against A, TM-score 1.00
- Q8C147 · AlphaFold monomer V2.0 prediction for dedicator of cytokinesis protein 8 (Q8C147) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain B 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 Q8C147
- Every structure of UniProt P60953
- Elsewhere: RCSB PDB 3VHL · PDBe 3VHL · UniProt Q8C147 · UniProt P60953
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