Hmdii from methanocaldococcus jannaschii reconstitued with fe- guanylylpyridinol (fegp) cofactor and co-crystallized with methenyl- tetrahydromethanopterin at 2.5 a resolution

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).

Ligands and binding sites

• FE9 · iron-guanylyl pyridinol cofactor · ligand · chains A
• E4M · 1-{4-[(6s,6ar,7r)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6, 6A,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol · ligand · chains A
• NA · Sodium ion · metal · chains A
• MG · Magnesium ion · metal · chains A
• SO4 · Sulfate ion · ion · 7 copies · chains A
• CL · Chloride ion · ion · chains A
• ACT · Acetate ion · additive · 9 copies · chains A
• EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Compared structures

• 6HUX · HmdII from Methanocaldococcus jannaschii reconstitued with Fe-guanylylpyridinol (FeGP)… · the same entry in another collection · chain A against A, TM-score 1.00
• Q58734 · AlphaFold monomer V2.0 prediction for H(2)-forming methylenetetrahydromethanopterin… · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q58734
• Elsewhere: RCSB PDB 6HUX · PDBe 6HUX · UniProt Q58734