› 7vld

X-ray diffraction
2.1Å resolution

Oxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation

Released:
DOI: 10.2210/pdb7vld/pdb
PDB entry 7vld coloured by chain, front view.
PDB entry 7vld coloured by chain, side view.
PDB entry 7vld coloured by chain, top view.
Source organism: Lamellibrachia satsuma
Primary publication:
Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Numoto N, Onoda S, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N
OpenAccess logo Biophys Physicobiol 19 1-10 (2022)
PMID: 35797404

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-197402 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Extracellular globin Chains: A, E
Molecule details ›
Chains: A, E
Length: 146 amino acids
Theoretical weight: 16.37 KDa
Source organism: Lamellibrachia satsuma
UniProt:
  • Canonical: S0BBU7 (Residues: 20-165; Coverage: 100%)
Gene name: v2hb-A1
Sequence domains: Globin
Extracellular globin Chains: B, F
Molecule details ›
Chains: B, F
Length: 144 amino acids
Theoretical weight: 15.95 KDa
Source organism: Lamellibrachia satsuma
UniProt:
  • Canonical: S0BBR6 (Residues: 17-160; Coverage: 100%)
Gene names: ghbA2, v2hb-A2
Sequence domains: Globin
Extracellular globin Chains: C, G
Molecule details ›
Chains: C, G
Length: 150 amino acids
Theoretical weight: 16.52 KDa
Source organism: Lamellibrachia satsuma
UniProt:
  • Canonical: S0BCU7 (Residues: 17-166; Coverage: 100%)
Gene names: ghbB2, v2hb-B2
Sequence domains: Globin
Extracellular globin Chains: D, H
Molecule details ›
Chains: D, H
Length: 149 amino acids
Theoretical weight: 16.23 KDa
Source organism: Lamellibrachia satsuma
UniProt:
  • Canonical: S0BAP9 (Residues: 20-168; Coverage: 100%)
Gene name: v2hb-B1
Sequence domains: Globin

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
3 bound ligands:
Ligand HEM 8 x HEM
Ligand OXY 8 x OXY
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P63
Unit cell:
a: 110.263Å b: 110.263Å c: 196.968Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.19 0.221

Quick links

Citations

1 mention without citation

Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Numoto et al. (2022)