7L3Y: Oxy-I107E CuB myoglobin

Crystal structure of oxy-I107E CuB myoglobin (I107E L29H F43H sperm whale myoglobin; partial occupancy). Determined by X-ray diffraction at 1.18 Å resolution. Released 3 Feb 2021.

Method: X-ray diffraction
Resolution: 1.18 Å
Organism: Physeter catodon
Chains: 1
Atoms: 1,626
Mol. weight: 18.08 kDa
Ligands: PER, HEM
Released: 3 Feb 2021

Explore 7L3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L3Y contains 12 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: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	4-17	14
α-helix	18-20	3
α-helix	21-35	15
α-helix	37-42	6
α-helix	44-46	3
α-helix	52-57	6
α-helix	59-77	19
α-helix	83-92	10
α-helix	93-97	5
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

>7L3Y_1 Myoglobin (chains A)
MVLSEGEWQLVLHVWAKVEADVAGHGQDIHIRLFKSHPETLEKHDRFKHLKTEAEMKASE
DLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFESEAIIHVLHSRH
PGDFGADAQGAMNKALELFRKDIAAKYKELGYQG

Ligands and cofactors

ID	Name	Formula	Copies
PER	Peroxide ion	O2	1
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1

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

Primary citation

An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network. Petrik, I.D., Davydov, R., Kahle, M. et al. Biochemistry (2021) 60:346-355. DOI 10.1021/acs.biochem.0c00852 · 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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