Research workbench
Crystal structure of the legionella pneumophila fic domain- containing effector ankx protein (inactive H229A mutant) in complex with cytidine-diphosphate-choline
Analyse Crystal structure of the legionella pneumophila fic domain- containing effector… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BET
- Type
- protein
- Length
- 959 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphocholine transferase ankx
- EC
- 2.7.1.-
- UniProt
- Q5ZXN6
- Ligands
- CDC, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphocholine transferase ankx (EC 2.7.1.-) | protein | 480 | 55% helix, 5% strand | Q5ZXN6 |
| B | Phosphocholine transferase ankx (EC 2.7.1.-) | protein | 479 | 55% helix, 5% strand | Q5ZXN6 |
Ligands and binding sites
- CDC · [2-cytidylate-O'-phosphonyloxyl]-ethyl-trimethyl-ammonium · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.71 | 0.77 | 65 | GOL |
| 2 | 771 | 0.70 | 0.76 | 67 | CDC, GOL |
| 3 | 302 | 0.63 | 0.80 | 33 | empty |
| 4 | 283 | 0.60 | 0.79 | 31 | CDC |
| 5 | 129 | 0.40 | 0.75 | 25 | SO4 |
Interfaces
1 interface between chains.
- A–B · 625 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4BET · Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5ZXN6 · AlphaFold monomer V2.0 prediction for phosphocholine transferase ankx (Q5ZXN6) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5ZXN6
- Elsewhere: RCSB PDB 4BET · PDBe 4BET · UniProt Q5ZXN6
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