MolNFT v1 · #165132 · protein
Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42
6TKY · Dedicator of cytokinesis protein 10: “Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42”. X-ray diffraction, 16 pockets (best druggability 0.75). MolNFT v1 #165132 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6TKY
- 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
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dedicator of cytokinesis protein 10 | protein | 416 | 54% helix, 15% strand | Q96BY6 |
| C | Cell division control protein 42 homolog (EC 3.6.5.2) | protein | 177 | 41% helix, 23% strand | P60953 |
| D | Cell division control protein 42 homolog (EC 3.6.5.2) | protein | 178 | 40% helix, 22% strand | P60953 |
| A | Dedicator of cytokinesis protein 10 | protein | 417 | 55% helix, 16% strand | Q96BY6 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.75 | 0.78 | 73 | empty |
| 2 | 958 | 0.74 | 0.77 | 70 | empty |
| 3 | 66 | 0.72 | 0.97 | 17 | empty |
| 4 | 563 | 0.70 | 0.79 | 69 | empty |
| 5 | 442 | 0.65 | 0.78 | 54 | empty |
Interfaces
3 interfaces between chains.
- C–A · 2150 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 2129 Ų buried · 27 hydrogen bonds · protein-protein
- B–A · 679 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6TKY · Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42 · the same entry in another collection · chain A against A, 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 0.93
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 6TKY · PDBe 6TKY · UniProt Q96BY6 · UniProt P60953
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