Structure of a methyltransferase complex

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 27% strand (DSSP).

Ligands and binding sites

• C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 4 copies · chains D, C
• SO4 · Sulfate ion · ion · 12 copies · chains A, C, B, D

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.

Interfaces

5 interfaces between chains.

• A–D · 1620 Ų buried · 26 hydrogen bonds · protein-protein
• B–C · 1567 Ų buried · 20 hydrogen bonds · protein-protein
• A–B · 445 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 435 Ų buried · 10 hydrogen bonds · protein-protein
• D–B · 354 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 5Y4R · Structure of a methyltransferase complex · the same entry in another collection · chain C against C, TM-score 1.00
• Q9HVI1 · AlphaFold monomer V2.0 prediction for cyclic diguanosine monophosphate-binding protein… · a predicted model of the same protein · chain C against A, TM-score 0.98
• O87131 · AlphaFold monomer V2.0 prediction for chemotaxis protein methyltransferase 1 (O87131) · a predicted model of the same protein · chain B against A, TM-score 0.77

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 O87131
• Every structure of UniProt Q9HVI1
• Elsewhere: RCSB PDB 5Y4R · PDBe 5Y4R · UniProt O87131 · UniProt Q9HVI1