› 2d2m

X-ray diffraction
2.85Å resolution

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

Released:
DOI: 10.2210/pdb2d2m/pdb
PDB entry 2d2m coloured by chain, front view.
PDB entry 2d2m coloured by chain, side view.
PDB entry 2d2m coloured by chain, top view.
Source organism: Oligobrachia mashikoi
Primary publication:
Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.
Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K
Proc Natl Acad Sci U S A 102 14521-6 (2005)
PMID: 16204001

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177350 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Extracellular giant hemoglobin major globin subunit A1 Chain: A
Molecule details ›
Chain: A
Length: 140 amino acids
Theoretical weight: 15.19 KDa
Source organism: Oligobrachia mashikoi
UniProt:
  • Canonical: Q7M419 (Residues: 17-156; Coverage: 100%)
Gene name: ghbA1
Sequence domains: Globin
Structure domains: Globins
Extracellular giant hemoglobin major globin subunit A2 Chain: B
Molecule details ›
Chain: B
Length: 142 amino acids
Theoretical weight: 15.33 KDa
Source organism: Oligobrachia mashikoi
UniProt:
  • Canonical: Q7M413 (Residues: 17-158; Coverage: 100%)
Gene name: ghbA2
Sequence domains: Globin
Structure domains: Globins
Extracellular giant hemoglobin major globin subunit B2 Chain: C
Molecule details ›
Chain: C
Length: 147 amino acids
Theoretical weight: 15.62 KDa
Source organism: Oligobrachia mashikoi
UniProt:
  • Canonical: Q7M418 (Residues: 17-163; Coverage: 100%)
Gene name: ghbB2
Sequence domains: Globin
Structure domains: Globins
Extracellular giant hemoglobin major globin subunit B1 Chain: D
Molecule details ›
Chain: D
Length: 145 amino acids
Theoretical weight: 14.79 KDa
Source organism: Oligobrachia mashikoi
UniProt:
  • Canonical: Q5KSB7 (Residues: 17-161; Coverage: 100%)
Gene name: ghbB1
Sequence domains: Globin
Structure domains: Globins

Ligands and Environments

2 bound ligands:
Ligand HEM 4 x HEM
Ligand OXY 4 x OXY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: R32
Unit cell:
a: 111.498Å b: 111.498Å c: 276.835Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.236 0.236 0.277

Quick links

Citations

3 review citations

Diversity of globin function: enzymatic, transport, storage, and sensing.
Vinogradov et al. (2008)
2 more

2 mentions without citation

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.
Numoto et al. (2005)
1 more