› 4ood

X-ray diffraction
1.24Å resolution

Structure of K42Y mutant of sperm whale myoglobin

Released:
DOI: 10.2210/pdb4ood/pdb
PDB entry 4ood coloured by chain, front view.
PDB entry 4ood coloured by chain, side view.
PDB entry 4ood coloured by chain, top view.
Source organism: Physeter catodon
Primary publication:
Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity.
Wang C, Lovelace LL, Sun S, Dawson JH, Lebioda L
Acta Crystallogr D Biol Crystallogr 70 2833-9 (2014)
PMID: 25372675

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-135409 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Myoglobin Chain: A
Molecule details ›
Chain: A
Length: 154 amino acids
Theoretical weight: 17.4 KDa
Source organism: Physeter catodon
Expression system: Escherichia coli
UniProt:
  • Canonical: P02185 (Residues: 1-154; Coverage: 100%)
Gene name: MB
Sequence domains: Globin
Structure domains: Globins

Ligands and Environments

3 bound ligands:
Ligand HEM 1 x HEM
Ligand SO4 6 x SO4
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 35.002Å b: 47.515Å c: 85.243Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.143 0.14 0.195
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network.
Kondo et al. (2023)

1 mention without citation

Water stabilizes an alternate turn conformation in horse heart myoglobin.
Bronstein et al. (2023)