A new catalytic mechanism of periplasmic nitrate reductase from desulfovibrio desulfuricans atcc 27774 from crystallographic and epr data and based on detailed analysis of the sixth ligand

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 19% 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
• SF4 · Iron/sulfur cluster · ligand · chains A
• LCP · Perchlorate ion · ligand · chains A
• MO · Molybdenum atom · metal · chains A
• UNX · Unknown atom or ion · ion · chains A

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

Pockets

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

Compared structures

• 2V45 · A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio… · the same entry in another collection · chain A against A, TM-score 1.00
• P81186 · AlphaFold monomer V2.0 prediction for periplasmic nitrate reductase (P81186) · a predicted model of the same protein · 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 P81186
• Elsewhere: RCSB PDB 2V45 · PDBe 2V45 · UniProt P81186