Crystal structure of deoxygenated hemoglobin in complex with an allosteric effector and nitric oxide

Structure

x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• RQ3 · 2-{4-[(3,5-dimethylanilino)-carbonyl-methyl]-phenoxy}-2-methylpropionic acid · ligand · 2 copies · chains A, C, D, B
• 5JN · 2-(nitrooxy)ethyl 2-(4-{2-[(3,5-dimethylphenyl)amino]-2-oxoethyl}phenoxy)-2-methylpropanoate · ligand · chains A, B, C
• NO · Nitric oxide · ion · 2 copies · chains A, C
• NO3 · Nitrate ion · ion · 2 copies · chains B, C, D
• CAC · Cacodylate ion · additive · chains B, 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, 5 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 844 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 840 Ų buried · 11 hydrogen bonds · protein-protein
• B–C · 711 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 698 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 294 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 5E29 · Crystal Structure of Deoxygenated Hemoglobin in Complex with an Allosteric Effector and… · the same entry in another collection · 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 P69905
• Every structure of UniProt P68871
• Elsewhere: RCSB PDB 5E29 · PDBe 5E29 · UniProt P69905 · UniProt P68871