X-ray reduced paraccocus denitrificans methylamine dehydrogenase O-quinone in complex with amicyanin.

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 44% strand (DSSP).

Ligands and binding sites

• CU · Copper (II) ion · metal · 2 copies · chains A, B
• GOL · Glycerol · additive · 4 copies · chains H, L, M

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

11 interfaces between chains.

• H–L · 1679 Ų buried · 33 hydrogen bonds · protein-protein
• J–M · 1672 Ų buried · 30 hydrogen bonds · protein-protein
• H–M · 1510 Ų buried · 24 hydrogen bonds · protein-protein
• J–L · 1480 Ų buried · 22 hydrogen bonds · protein-protein
• H–J · 698 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 2 modified (disulfide, cofactor).

Compared structures

• 2J55 · X-ray reduced Paraccocus denitrificans methylamine dehydrogenase O- qui in complex with… · the same entry in another collection · chain M against M, TM-score 1.00
• P22364 · AlphaFold monomer V2.0 prediction for amicyanin (P22364) · a predicted model of the same protein · chain B against A, TM-score 0.99
• P22619 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase light chain (P22619) · a predicted model of the same protein · chain L against A, TM-score 0.99
• P29894 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase heavy chain (P29894) · a predicted model of the same protein · chain J against A, TM-score 0.98

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 P22364
• Every structure of UniProt P29894
• Every structure of UniProt P22619
• Elsewhere: RCSB PDB 2J55 · PDBe 2J55 · UniProt P22364 · UniProt P29894 · UniProt P22619