The crystal structure of I-dmoi E117A in complex with its target DNA and in the presence of 2MM mn

Structure

x-ray diffraction · 5 distinct chains · 50% helix, 25% strand (DSSP).

Ligands and binding sites

• MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I
• CL · Chloride ion · ion · 7 copies · chains A, D, E, F, G, H
• ACT · Acetate ion · additive · 5 copies · chains A, B, C, D, E, F, G, H, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

15 interfaces between chains.

• E–F · 1302 Ų buried · 110 hydrogen bonds · nucleic-nucleic
• H–I · 1300 Ų buried · 108 hydrogen bonds · nucleic-nucleic
• B–C · 1298 Ų buried · 105 hydrogen bonds · nucleic-nucleic
• D–E · 1259 Ų buried · 30 hydrogen bonds · protein-nucleic
• G–H · 1247 Ų buried · 34 hydrogen bonds · protein-nucleic

Compared structures

• 5A0W · The crystal structure of I-dmoi E117A in complex with its target DNA and in the presence… · the same entry in another collection · chain I against I, TM-score 1.00
• P21505 · AlphaFold monomer V2.0 prediction for homing endonuclease I-dmoi (P21505) · a predicted model of the same protein · chain G against A, TM-score 1.00

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 P21505
• Elsewhere: RCSB PDB 5A0W · PDBe 5A0W · UniProt P21505