Research workbench
Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42
Analyse Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TKZ
- Type
- protein
- Length
- 1,188 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dedicator of cytokinesis protein 10; Cell division control protein 42 homolog
- EC
- 3.6.5.2
- UniProt
- Q96BY6, P60953
- Ligands
- GDP
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dedicator of cytokinesis protein 10 | protein | 416 | 53% helix, 15% strand | Q96BY6 |
| C | Cell division control protein 42 homolog (EC 3.6.5.2) | protein | 177 | 39% helix, 22% strand | P60953 |
| D | Cell division control protein 42 homolog (EC 3.6.5.2) | protein | 178 | 41% helix, 22% strand | P60953 |
| A | Dedicator of cytokinesis protein 10 | protein | 417 | 55% helix, 16% strand | Q96BY6 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains C, B, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.74 | 0.77 | 72 | empty |
| 2 | 1023 | 0.74 | 0.77 | 97 | empty |
| 3 | 931 | 0.73 | 0.77 | 65 | empty |
| 4 | 98 | 0.72 | 0.94 | 17 | empty |
| 5 | 608 | 0.64 | 0.75 | 58 | empty |
Interfaces
3 interfaces between chains.
- B–D · 2136 Ų buried · 24 hydrogen bonds · protein-protein
- C–A · 2050 Ų buried · 23 hydrogen bonds · protein-protein
- B–A · 742 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6TKZ · Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42 · the same entry in another collection · chain B against B, TM-score 1.00
- Q96BY6 · AlphaFold monomer V2.0 prediction for dedicator of cytokinesis protein 10 (Q96BY6) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain D 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 Q96BY6
- Every structure of UniProt P60953
- Elsewhere: RCSB PDB 6TKZ · PDBe 6TKZ · UniProt Q96BY6 · UniProt P60953
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