› 3d1k

X-ray diffraction
1.25Å resolution

R/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) state

Released:
DOI: 10.2210/pdb3d1k/pdb
PDB entry 3d1k coloured by chain, front view.
PDB entry 3d1k coloured by chain, side view.
PDB entry 3d1k coloured by chain, top view.
Source organism: Trematomus newnesi
Primary publication:
Spectroscopic and crystallographic characterization of a tetrameric hemoglobin oxidation reveals structural features of the functional intermediate relaxed/tense state.
Vitagliano L, Vergara A, Bonomi G, Merlino A, Verde C, di Prisco G, Howes BD, Smulevich G, Mazzarella L
J Am Chem Soc 130 10527-35 (2008)
PMID: 18642904

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155333 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Hemoglobin subunit alpha-1 Chain: A
Molecule details ›
Chain: A
Length: 142 amino acids
Theoretical weight: 15.68 KDa
Source organism: Trematomus newnesi
UniProt:
  • Canonical: P45718 (Residues: 1-142; Coverage: 100%)
Gene name: hba1
Sequence domains: Globin
Structure domains: Globins
Hemoglobin subunit beta-1/2 Chain: B
Molecule details ›
Chain: B
Length: 146 amino acids
Theoretical weight: 16.25 KDa
Source organism: Trematomus newnesi
UniProt:
  • Canonical: P45720 (Residues: 1-146; Coverage: 100%)
Sequence domains: Globin
Structure domains: Globins

Ligands and Environments

3 bound ligands:
Ligand ACE 1 x ACE
Ligand CMO 1 x CMO
Ligand HEM 2 x HEM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: C2
Unit cell:
a: 88.458Å b: 87.664Å c: 55.502Å
α: 90° β: 99.16° γ: 90°
R-values:
R R work R free
0.167 0.167 0.202

Quick links

Citations

3 review citations

Occurrence and formation of endogenous histidine hexa-coordination in cold-adapted hemoglobins.
Merlino et al. (2011)
2 more

2 mentions without citation

Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States.
Balasco et al. (2021)
1 more