Crystal structure of partially reduced periplasmic nitrate reductase from cupriavidus necator using ionic liquids

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).

Ligands and binding sites

• MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 2 copies · chains A
• HEC · Heme C · ligand · 2 copies · chains B, A
• SF4 · Iron/sulfur cluster · ligand · chains A
• MOS · Dioxothiomolybdenum(vi) ion · ligand · chains A
• CL · Chloride ion · ion · chains A, B
• FMT · Formic acid · additive · 19 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 3067 Ų buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor, 1 modified (heme c attachment, oxidation).

Compared structures

• 3O5A · Crystal Structure of partially reduced Periplasmic Nitrate Reductase from Cupriavidus… · the same entry in another collection · chain A against A, TM-score 1.00
• P39185 · AlphaFold monomer V2.0 prediction for periplasmic nitrate reductase (P39185) · a predicted model of the same protein · chain A against A, TM-score 1.00
• P39186 · AlphaFold monomer V2.0 prediction for periplasmic nitrate reductase, electron transfer… · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P39185
• Every structure of UniProt P39186
• Elsewhere: RCSB PDB 3O5A · PDBe 3O5A · UniProt P39185 · UniProt P39186