Research workbench
Crystal structure of the dhr-2 domain of DOCK2 in complex with RAC1 (T17N mutant)
Analyse Crystal structure of the dhr-2 domain of DOCK2 in complex with RAC1 (T17N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B13
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dedicator of cytokinesis protein 2; RAS-related C3 botulinum toxin substrate 1
- UniProt
- Q92608, P63000
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dedicator of cytokinesis protein 2 | protein | 427 | 55% helix, 16% strand | Q92608 |
| B, D | RAS-related C3 botulinum toxin substrate 1 | protein | 177 | 38% helix, 23% strand | P63000 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.80 | 0.82 | 79 | empty |
| 2 | 1003 | 0.80 | 0.81 | 83 | empty |
| 3 | 100 | 0.77 | 0.97 | 21 | empty |
| 4 | 87 | 0.75 | 0.97 | 20 | empty |
| 5 | 271 | 0.64 | 0.81 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1954 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1849 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1216 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3B13 · Crystal structure of the DHR-2 domain of DOCK2 in complex with Rac1 (T17N mutant) · the same entry in another collection · chain B against B, TM-score 1.00
- Q92608 · AlphaFold monomer V2.0 prediction for dedicator of cytokinesis protein 2 (Q92608) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P63000 · AlphaFold monomer V2.0 prediction for RAS-related C3 botulinum toxin substrate 1 (P63000) · a predicted model of the same protein · chain B 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 Q92608
- Every structure of UniProt P63000
- Elsewhere: RCSB PDB 3B13 · PDBe 3B13 · UniProt Q92608 · UniProt P63000
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