› 5x2t

X-ray diffraction
2.64Å resolution

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 4 mM bezafibrate pH 7.2.

Released:
DOI: 10.2210/pdb5x2t/pdb
PDB entry 5x2t coloured by chain, front view.
PDB entry 5x2t coloured by chain, side view.
PDB entry 5x2t coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Direct observation of conformational population shifts in crystalline human hemoglobin.
Shibayama N, Ohki M, Tame JRH, Park SY
J Biol Chem 292 18258-18269 (2017)
PMID: 28931607

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159519 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Hemoglobin subunit alpha Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
Length: 141 amino acids
Theoretical weight: 15.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P69905 (Residues: 2-142; Coverage: 99%)
Gene names: HBA1, HBA2
Sequence domains: Globin
Structure domains: Globins
Hemoglobin subunit beta Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
Length: 146 amino acids
Theoretical weight: 15.89 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P68871 (Residues: 2-147; Coverage: 99%)
Gene name: HBB
Sequence domains: Globin
Structure domains: Globins

Ligands and Environments

3 bound ligands:
Ligand HNI 6 x HNI
Ligand HEM 6 x HEM
Ligand PEM 1 x PEM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2
Unit cell:
a: 228.494Å b: 55.024Å c: 138.504Å
α: 90° β: 103.38° γ: 90°
R-values:
R R work R free
0.234 0.232 0.277

Quick links

Citations

3 citation in other articles

Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.
Numoto et al. (2021)
2 more

1 mention without citation

Direct observation of conformational population shifts in crystalline human hemoglobin.
Shibayama et al. (2017)