Structure of hba with compound 23 (pf-07059013)

Structure

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

Ligands and binding sites

• O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 5 copies · chains A, B, C, D
• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• VUD · 6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)pyridin-2(1H)-one · 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

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

Interfaces

6 interfaces between chains.

• A–B · 954 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 930 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 457 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 445 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 423 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 7JY3 · Structure of HbA with compound 23 (PF-07059013) · 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 C 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 7JY3 · PDBe 7JY3 · UniProt P69905 · UniProt P68871