High resolution structure of native hydrogenase (hyd-1)

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

Ligands and binding sites

• SF4 · Iron/sulfur cluster · ligand · 2 copies · chains S, T
• F3S · FE3-S4 cluster · ligand · 2 copies · chains S, L, T, M
• SF3 · FE4-S3 cluster · ligand · 2 copies · chains S, L, T, M
• FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains L, M
• NI · Nickel (II) ion · metal · 2 copies · chains L, M
• MG · Magnesium ion · metal · 2 copies · chains L, M
• LI · Lithium ion · metal · chains L
• CL · Chloride ion · ion · 2 copies · chains S, T
• SO4 · Sulfate ion · ion · 2 copies · chains S, L, M
• LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains S, T

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• T–M · 4047 Ų buried · 67 hydrogen bonds · protein-protein
• S–L · 4032 Ų buried · 68 hydrogen bonds · protein-protein
• S–M · 869 Ų buried · 7 hydrogen bonds · protein-protein
• L–T · 831 Ų buried · 9 hydrogen bonds · protein-protein
• S–T · 702 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

• P0ACD8 · AlphaFold monomer V2.0 prediction for hydrogenase-1 large chain (P0ACD8) · a predicted model of the same protein · chain L against A, TM-score 1.00
• P69740 · AlphaFold monomer V2.0 prediction for hydrogenase-1 small chain (P69740) · a predicted model of the same protein · chain S 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 P69740
• Every structure of UniProt P0ACD8
• Elsewhere: RCSB PDB 6FPO · PDBe 6FPO · UniProt P69740 · UniProt P0ACD8