Research workbench
Crystal structure of the legionella pneumophila fic domain-containing effector ankx protein in complex with cytidine monophosphate
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
- 4BER
- Type
- protein
- Length
- 950 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
- C5P, PO4
- Pockets
- 10 · best druggability 0.69
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 | 475 | 56% helix, 5% strand | Q5ZXN6 |
| B | Phosphocholine transferase ankx (EC 2.7.1.-) | protein | 475 | 55% helix, 5% strand | Q5ZXN6 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.69 | 0.76 | 71 | empty |
| 2 | 406 | 0.65 | 0.79 | 38 | empty |
| 3 | 320 | 0.61 | 0.78 | 26 | empty |
| 4 | 258 | 0.60 | 0.80 | 29 | C5P, PO4 |
| 5 | 299 | 0.60 | 0.78 | 30 | C5P, PO4 |
Interfaces
1 interface between chains.
- A–B · 617 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4BER · 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 A 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 4BER · PDBe 4BER · UniProt Q5ZXN6
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