Crystal structure of the heterodimeric nitrate reductase from rhodobacter sphaeroides

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 17% 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 · 16 copies · chains A, C, E, G, I, K, M, O
• HEC · Heme C · ligand · 16 copies · chains B, D, A, F, C, H, P, E, N, G, J, L, I, K, M, O
• SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, C, E, G, I, K, M, O
• MO · Molybdenum atom · metal · 8 copies · chains A, C, E, G, I, K, M, O

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

51 interfaces between chains.

• I–J · 3098 Ų buried · 39 hydrogen bonds · protein-protein
• C–D · 3088 Ų buried · 40 hydrogen bonds · protein-protein
• K–L · 3084 Ų buried · 37 hydrogen bonds · protein-protein
• G–H · 3084 Ų buried · 37 hydrogen bonds · protein-protein
• M–N · 3080 Ų buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 cofactor (heme c attachment).

Compared structures

• 1OGY · Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides · the same entry in another collection · chain P against P, 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 Q53176
• Every structure of UniProt Q53177
• Elsewhere: RCSB PDB 1OGY · PDBe 1OGY · UniProt Q53176 · UniProt Q53177