Crystal structure of actin in complex with lobophorolide

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).

Ligands and binding sites

• ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
• LO3 · (1S,3S,4S,5S,7R,8S,9R,12E,14E,16R,17R,19R)-16-hydroxy-9-{(1S,2S,3S)-2-hydroxy-5-[(2S,4R,6S)-4-methoxy-6-methyltetrahydro-2H-pyran-2-yl]-1,3-dimethylpentyl}-3,5,7,17-tetramethoxy-8,14-dimethyl-11H-spiro[10,23-dioxabicyclo[17.3.1]tricosa-12,14,20-triene-4,2'-oxiran]-11-one · ligand · 2 copies · chains A, B
• CA · Calcium ion · metal · 4 copies · chains A, B
• MG · Magnesium ion · metal · 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.

Interfaces

1 interface between chains.

• A–B · 79 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 3M6G · Crystal structure of actin in complex with lobophorolide · the same entry in another collection · chain A against A, TM-score 1.00
• P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P68135
• Elsewhere: RCSB PDB 3M6G · PDBe 3M6G · UniProt P68135