5YCE: Sperm whale myoglobin swMb

Sperm whale myoglobin swMb. Determined by X-ray diffraction at 0.77 Å resolution. Released 19 Sept 2018.

Method: X-ray diffraction
Resolution: 0.77 Å
Organism: Physeter catodon
Chains: 1
Atoms: 2,195
Mol. weight: 18.27 kDa
Ligands: HEM
Released: 19 Sept 2018

Explore 5YCE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YCE contains 10 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	4-14	11
α-helix	15-20	6
α-helix	21-35	15
α-helix	37-41	5
α-helix	52-56	5
α-helix	59-76	18
α-helix	83-95	13
α-helix	101-118	18
α-helix	120-122	3
α-helix	125-148	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myoglobin	A	protein	154	Physeter catodon	P02185 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YCE_1 Myoglobin (chains A)
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASE
DLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH
PGDFGADAQGAMNKALELFRKDIAAKYKELGYQG

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Tracing whale myoglobin evolution by resurrecting ancient proteins. Isogai, Y., Imamura, H., Nakae, S. et al. Sci Rep (2018) 8:16883-16883. DOI 10.1038/s41598-018-34984-6 · PubMed

Other PDB entries of the same protein (UniProt P02185 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7VDN 0.93 Å, High resolution crystal structure of Sperm Whale Myoglobin in the carbonmonoxy form
1A6M 1.0 Å, Oxy-myoglobin, atomic resolution
1NAZ 1.04 Å, structure of microgravity-grown oxidized myoglobin mutant YQR (ISS8A)
8ESU 1.04 Å, Myoglobin variant Mb-imi complex
1A6K 1.1 Å, Aquomet-myoglobin, atomic resolution
2EKT 1.1 Å, Crystal structure of myoglobin reconstituted with 6-methyl-6-depropionatehemin
3O89 1.1 Å, Crystal Structure of Sperm Whale Myoglobin G65T
6M8F 1.1 Å, Engineered sperm whale myoglobin-based carbene transferase
9P1F 1.1 Å, Myoglobin variant RR22 in complex with imidazole
4H07 1.14 Å, Complex of G65T Myoglobin with Phenol in its Proximal Cavity
1A6G 1.15 Å, Carbonmonoxy-myoglobin, atomic resolution
1A6N 1.15 Å, Deoxy-myoglobin, atomic resolution

Browse structure collections

About this viewer

MolViewer shows 5YCE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.