MolNFT v1 · #171215 · protein
Structure of drra from legionella pneumophilia in complex with human RAB8A
6YX5 · RAS-related protein rab-8A: “Structure of drra from legionella pneumophilia in complex with human RAB8A”. X-ray diffraction, 5 ligands (GNP, LJN, GLC), 7 pockets (best druggability 0.78). MolNFT v1 #171215 on GenesisL1: 3D…
- PDB
- 6YX5
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-8A; Multifunctional virulence effector protein drra
- UniProt
- A0A1U7REJ8, Q29ST3
- Ligands
- GNP, LJN, GLC, MG, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-8A | protein | 173 | 37% helix, 28% strand | A0A1U7REJ8 |
| B | Multifunctional virulence effector protein drra | protein | 339 | 60% helix, 6% strand | Q29ST3 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- LJN · [(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2, 3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.78 | 0.83 | 94 | MG, GNP |
| 2 | 120 | 0.63 | 0.87 | 16 | GLC |
| 3 | 312 | 0.59 | 0.78 | 32 | GLC, SO4 |
| 4 | 100 | 0.43 | 0.78 | 13 | empty |
| 5 | 105 | 0.43 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1182 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6YX5 · Structure of DrrA from Legionella pneumophilia in complex with human Rab8a · the same entry in another collection · chain A against A, TM-score 1.00
- Q29ST3 · AlphaFold monomer V2.0 prediction for multifunctional virulence effector protein drra… · a predicted model of the same protein · chain B against A, TM-score 1.00
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 A0A1U7REJ8
- Every structure of UniProt Q29ST3
- Elsewhere: RCSB PDB 6YX5 · PDBe 6YX5 · UniProt A0A1U7REJ8 · UniProt Q29ST3
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