MolNFT v1 · #172130 · protein
The mechanism of activation of the actin binding protein EHBP1 by RAB8 family members.
6ZSI · 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 0.68). MolNFT v1 #172130 on GenesisL1: 3D…
- PDB
- 6ZSI
- Type
- protein
- Length
- 607 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 0.68
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-8A | protein | 171 | 36% 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 | 85% helix, 0% strand | Q8NDI1 |
| D | Eh domain-binding protein 1 | protein | 133 | 88% 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
- PEG · Di(hydroxyethyl)ether · additive · 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 | 422 | 0.68 | 0.80 | 56 | GNP, MG |
| 2 | 449 | 0.68 | 0.79 | 53 | GNP, MG |
| 3 | 459 | 0.63 | 0.76 | 47 | empty |
| 4 | 57 | 0.27 | 0.73 | 11 | empty |
| 5 | 53 | 0.26 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–D · 897 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 764 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 396 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6ZSI · The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. · the same entry in another collection · chain B against B, 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 0.85
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 6ZSI · PDBe 6ZSI · UniProt P61006 · UniProt Q8NDI1
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