MolNFT v1 · #172131 · protein
The mechanism of activation of the actin binding protein EHBP1 by RAB8 family members.
6ZSJ · RAS-related protein rab-8A: “The mechanism of activation of the actin binding protein EHBP1 by RAB8 family members.”. X-ray diffraction, 2 ligands (GNP, MG), 5 pockets (best druggability 0.70). MolNFT v1 #172131 on GenesisL1: 3D…
- 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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