Research workbench
The mechanism of activation of the actin binding protein EHBP1 by RAB8 family members
Analyse The mechanism of activation of the actin binding protein EHBP1 by RAB8 family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZSH
- Type
- protein
- Length
- 388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eh domain-binding protein 1
- UniProt
- Q8NDI1
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eh domain-binding protein 1 | protein | 92 | 93% helix, 0% strand | Q8NDI1 |
| B | Eh domain-binding protein 1 | protein | 108 | 59% helix, 0% strand | Q8NDI1 |
| C | Eh domain-binding protein 1 | protein | 82 | 91% helix, 0% strand | Q8NDI1 |
| D | Eh domain-binding protein 1 | protein | 106 | 58% helix, 0% strand | Q8NDI1 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.49 | 0.77 | 26 | empty |
| 2 | 162 | 0.44 | 0.75 | 22 | empty |
| 3 | 67 | 0.32 | 0.75 | 14 | empty |
| 4 | 50 | 0.26 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 627 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 561 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 176 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6ZSH · The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members · the same entry in another collection · chain D against D, TM-score 1.00
- Q8NDI1 · AlphaFold monomer V2.0 prediction for eh domain-binding protein 1 (Q8NDI1) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q8NDI1
- Elsewhere: RCSB PDB 6ZSH · PDBe 6ZSH · UniProt Q8NDI1
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