Research workbench
Structural basis for PI(4)P-specific membrane recruitment of the legionella pneumophila effector DRRA/SIDM
Analyse Structural basis for PI(4)P-specific membrane recruitment of the legionella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MXP
- Type
- protein
- Length
- 310 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Defects in RAB1 recruitment protein a
- EC
- 2.7.7.-
- UniProt
- Q5ZSQ3
- Ligands
- DB4, NA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Defects in RAB1 recruitment protein a (EC 2.7.7.-) | protein | 310 | 65% helix, 1% strand | Q5ZSQ3 |
Ligands and binding sites
- DB4 · (2R)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.57 | 0.79 | 36 | empty |
| 2 | 136 | 0.55 | 0.82 | 26 | empty |
| 3 | 54 | 0.33 | 0.78 | 17 | empty |
Compared structures
- 4MXP · Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5ZSQ3 · AlphaFold monomer V2.0 prediction for multifunctional virulence effector protein drra… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q5ZSQ3
- Elsewhere: RCSB PDB 4MXP · PDBe 4MXP · UniProt Q5ZSQ3
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