Carbonmonoxy hemoglobin in complex with the antisickling agent 2- hydroxy-6-((6-(HYDROXYMETHYL)PYRIDIN-2-YL)METHOXY)BENZALDEHYDE (VZHE039)

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• V39 · 3-{[6-(hydroxymethyl)pyridin-2-yl]methoxy}-2-methylphenol · ligand · 2 copies · chains A, C
• CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 899 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 897 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 485 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 430 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 398 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6XD9 · Carbonmonoxy hemoglobin in complex with the antisickling agent… · the same entry in another collection · chain D against D, TM-score 1.00
• P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain D against A, TM-score 0.98
• P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 6XD9 · PDBe 6XD9 · UniProt P69905 · UniProt P68871