› 5ksi

X-ray diffraction
1.8Å resolution

Crystal structure of deoxygenated hemoglobin in complex with sphingosine phosphate and 2,3-Bisphosphoglycerate

Released:
DOI: 10.2210/pdb5ksi/pdb
PDB entry 5ksi coloured by chain, front view.
PDB entry 5ksi coloured by chain, side view.
PDB entry 5ksi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and Functional Insight of Sphingosine 1-Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease.
Sun K, D'Alessandro A, Ahmed MH, Zhang Y, Song A, Ko TP, Nemkov T, Reisz JA, Wu H, Adebiyi M, Peng Z, Gong J, Liu H, Huang A, Wen YE, Wen AQ, Berka V, Bogdanov MV, Abdulmalik O, Han L, Tsai AL, Idowu M, Juneja HS, Kellems RE, Dowhan W, Hansen KC, Safo MK, Xia Y
OpenAccess logo Sci Rep 7 15281 (2017)
PMID: 29127281

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
Molecule details ›
Chains: A, C
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
Molecule details ›
Chains: B, D
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 HEM 4 x HEM
Ligand S1P 5 x S1P
Ligand DG2 2 x DG2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: Cu FINE FOCUS
Spacegroup: P21212
Unit cell:
a: 95.94Å b: 98.08Å c: 65.14Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.18 0.22

Quick links

Citations

8 review citations

Hemoglobin: Structure, Function and Allostery.
Ahmed et al. (2020)
7 more

1 mention without citation

Structural and Functional Insight of Sphingosine 1-Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease.
Sun et al. (2017)