Crystallographic analysis of the interaction of nitric oxide with hemoglobin from trematomus bernacchii in the T quaternary structure (fully ligated state).

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• ACE · Acetyl group · ligand · 2 copies · chains A, C
• NO · Nitric oxide · ion · 4 copies · chains A, B, C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• C–D · 829 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 796 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 724 Ų buried · 13 hydrogen bonds · protein-protein
• B–C · 646 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 451 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 4G51 · Crystallographic analysis of the interaction of nitric oxide with hemoglobin from… · the same entry in another collection · chain A against A, TM-score 1.00
• P80043 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P80043) · a predicted model of the same protein · chain A against A, TM-score 0.99
• P80044 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P80044) · a predicted model of the same protein · chain B 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 P80043
• Every structure of UniProt P80044
• Elsewhere: RCSB PDB 4G51 · PDBe 4G51 · UniProt P80043 · UniProt P80044