8ESU: Myoglobin variant Mb-imi complex

Myoglobin variant Mb-imi complex. Determined by X-ray diffraction at 1.04 Å resolution. Released 6 Dec 2023.

Method: X-ray diffraction
Resolution: 1.04 Å
Organism: Physeter catodon
Chains: 1
Atoms: 1,604
Mol. weight: 18.13 kDa
Ligands: HEM
Released: 6 Dec 2023

Explore 8ESU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ESU contains 9 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: 9 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	83-91	9
α-helix	92-97	6
α-helix	101-118	18
α-helix	125-149	25

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>8ESU_1 Myoglobin (chains A)
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASE
DLKKGGVTALTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH
PGNFGADAQGAMNKALELFRKDIAAKYKELGYQG

Ligands and cofactors

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

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

Primary citation

Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone. Nam, D., Bacik, J.P., Khade, R.L. et al. Nat Commun (2023) 14:7985-7985. DOI 10.1038/s41467-023-43559-7 · 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)
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

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