Crystal structure of carbon monoxy hemoglobin in complex with 5HMF at 1.8 ångström

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• MW0 · (5-methylfuran-2-yl)methanol · ligand · 2 copies · chains A, C
• OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D

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

Pockets

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

Interfaces

6 interfaces between chains.

• A–B · 929 Ų buried · 10 hydrogen bonds · protein-protein
• C–D · 884 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 455 Ų buried · 5 hydrogen bonds · protein-protein
• A–D · 430 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 380 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7UD8 · Crystal structure of carbon monoxy Hemoglobin in complex with 5HMF at 1.8 Angstrom · 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 7UD8 · PDBe 7UD8 · UniProt P69905 · UniProt P68871