Crystal structure of [fe]-hydrogenase (hmd) from methanococcus aeolicus in complex with fegp cofactor and methenyl- tetrahydromethanopterin (close form B)

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 11% strand (DSSP).

Ligands and binding sites

• 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 · 2 copies · chains A, K
• FE9 · iron-guanylyl pyridinol cofactor · ligand · 2 copies · chains A, K
• K · Potassium ion · metal · 4 copies · chains A, K
• NA · Sodium ion · metal · 2 copies · chains A, K
• SCN · Thiocyanate ion · ion · 15 copies · chains A, K
• CL · Chloride ion · ion · 2 copies · chains A, K
• GOL · Glycerol · additive · 2 copies · chains A, K
• 2PE · Nonaethylene glycol · additive · chains K

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

Pockets

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

Interfaces

1 interface between chains.

• A–K · 4515 Ų buried · 44 hydrogen bonds · protein-protein

Compared structures

• 6HAE · Crystal structure of [Fe]-hydrogenase (Hmd) from Methanococcus aeolicus in complex with… · the same entry in another collection · chain A 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 A6UVT1
• Elsewhere: RCSB PDB 6HAE · PDBe 6HAE · UniProt A6UVT1