7SPF: Sperm whale myoglobin variant sMb5(pCaaF)

Crystal structure of sperm whale myoglobin variant sMb5(pCaaF). Determined by X-ray diffraction at 1.17 Å resolution. Released 1 Jun 2022.

Method: X-ray diffraction
Resolution: 1.17 Å
Organism: Physeter catodon
Chains: 1
Atoms: 1,419
Mol. weight: 18.62 kDa
Ligands: HEM, OXY
Released: 1 Jun 2022

Explore 7SPF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SPF contains 8 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	4-17	14
α-helix	21-35	15
α-helix	37-42	6
α-helix	52-57	6
α-helix	59-77	19
α-helix	83-95	13
α-helix	101-118	18
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

>7SPF_1 Myoglobin (chains A)
MVLSEXEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASE
DLKKVGVTALTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH
PGNFGACAQGAMNKALELFRKDIAAKYKELGYQG

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1
OXY	Oxygen molecule	O2	1

Water and common crystallization additives (NO3, SO4) are not listed.

Primary citation

Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization. Iannuzzelli, J.A., Bacik, J.P., Moore, E.J. et al. Biochemistry (2022) 61:1041-1054. DOI 10.1021/acs.biochem.2c00033 · PubMed

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

5YCE 0.77 Å, Sperm whale myoglobin swMb
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

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