MolNFT v1 · #176512 · protein
Cryo-EM structure of the human ELMO1-DOCK5-RAC1 complex
7DPA · Dedicator of cytokinesis protein 5: “Cryo-EM structure of the human ELMO1-DOCK5-RAC1 complex”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #176512 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DPA
- Type
- protein
- Length
- 4,034 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dedicator of cytokinesis protein 5; RAS-related C3 botulinum toxin substrate 1…
- EC
- 3.6.5.2
- UniProt
- Q9H7D0, P63000, Q92556
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dedicator of cytokinesis protein 5 | protein | 1642 | 48% helix, 7% strand | Q9H7D0 |
| B, E | RAS-related C3 botulinum toxin substrate 1 (EC 3.6.5.2) | protein | 177 | 33% helix, 13% strand | P63000 |
| C, F | Engulfment and cell motility protein 1 | protein | 198 | 29% helix, 12% strand | Q92556 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.86 | 0.90 | 77 | empty |
| 2 | 921 | 0.84 | 0.85 | 105 | empty |
| 3 | 751 | 0.83 | 0.86 | 83 | empty |
| 4 | 960 | 0.83 | 0.84 | 99 | empty |
| 5 | 309 | 0.83 | 0.92 | 43 | empty |
Interfaces
7 interfaces between chains.
- A–C · 2536 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 2514 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1799 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1798 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1027 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7DPA · Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q92556 · AlphaFold monomer V2.0 prediction for engulfment and cell motility protein 1 (Q92556) · a predicted model of the same protein · chain C against A, TM-score 0.84
- Q9H7D0 · AlphaFold monomer V2.0 prediction for dedicator of cytokinesis protein 5 (Q9H7D0) · a predicted model of the same protein · chain D against A, TM-score 0.78
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 Q9H7D0
- Every structure of UniProt P63000
- Every structure of UniProt Q92556
- Elsewhere: RCSB PDB 7DPA · PDBe 7DPA · UniProt Q9H7D0 · UniProt P63000 · UniProt Q92556
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