Research workbench
Structure of the complex between DOCK9 and CDC42.
Analyse Structure of the complex between DOCK9 and CDC42. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WM9
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dedicator of cytokinesis protein 9; Cell division control protein 42 homolog
- UniProt
- Q9BZ29, P60953
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dedicator of cytokinesis protein 9 | protein | 407 | 56% helix, 15% strand | Q9BZ29 |
| B | Cell division control protein 42 homolog | protein | 179 | 39% helix, 22% strand | P60953 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.74 | 0.77 | 79 | empty |
| 2 | 122 | 0.50 | 0.80 | 24 | empty |
| 3 | 55 | 0.43 | 0.83 | 16 | empty |
| 4 | 50 | 0.29 | 0.76 | 17 | empty |
| 5 | 56 | 0.27 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2354 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2WM9 · Structure of the complex between DOCK9 and Cdc42. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BZ29 · AlphaFold monomer V2.0 prediction for dedicator of cytokinesis protein 9 (Q9BZ29) · a predicted model of the same protein · chain A against A, TM-score 0.99
- 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 Q9BZ29
- Every structure of UniProt P60953
- Elsewhere: RCSB PDB 2WM9 · PDBe 2WM9 · UniProt Q9BZ29 · UniProt P60953
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