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
- 6ZSJ
- Type
- protein
- Length
- 606 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-8A; Eh domain-binding protein 1
- UniProt
- P61006, Q8NDI1
- Ligands
- GNP, MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-8A | protein | 171 | 37% helix, 28% strand | P61006 |
| B | RAS-related protein rab-8A | protein | 173 | 37% helix, 28% strand | P61006 |
| C | Eh domain-binding protein 1 | protein | 130 | 88% helix, 0% strand | Q8NDI1 |
| D | Eh domain-binding protein 1 | protein | 132 | 89% helix, 0% strand | Q8NDI1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.70 | 0.80 | 61 | GNP, MG |
| 2 | 361 | 0.66 | 0.80 | 42 | GNP, MG |
| 3 | 450 | 0.62 | 0.76 | 52 | empty |
| 4 | 54 | 0.30 | 0.75 | 11 | empty |
| 5 | 57 | 0.29 | 0.75 | 10 | empty |
Interfaces
3 interfaces between chains.
- B–D · 912 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 845 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 424 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6ZSJ · 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
- P61006 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-8A (P61006) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q8NDI1 · AlphaFold monomer V2.0 prediction for eh domain-binding protein 1 (Q8NDI1) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 P61006
- Every structure of UniProt Q8NDI1
- Elsewhere: RCSB PDB 6ZSJ · PDBe 6ZSJ · UniProt P61006 · UniProt Q8NDI1
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