7VDN: Sperm Whale Myoglobin in the carbonmonoxy form

High resolution crystal structure of Sperm Whale Myoglobin in the carbonmonoxy form. Determined by X-ray diffraction at 0.93 Å resolution. Released 14 Sept 2022.

Method: X-ray diffraction
Resolution: 0.93 Å
Organism: Physeter catodon
Chains: 1
Atoms: 1,394
Mol. weight: 17.98 kDa
Ligands: HEM, CMO
Released: 14 Sept 2022

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

Secondary structure: helices and β-sheets

7VDN contains 11 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: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	4-17	14
α-helix	18-20	3
α-helix	21-35	15
α-helix	37-40	4
α-helix	52-57	6
α-helix	59-77	19
α-helix	83-91	9
α-helix	92-96	5
α-helix	101-118	18
α-helix	120-122	3
α-helix	125-149	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myoglobin	A	protein	151	Physeter catodon	P02185 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7VDN_1 Myoglobin (chains A)
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGY

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1
CMO	Carbon monoxide	C O	1

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

Primary citation

X-ray fluorescence holography of biological metal sites: Application to myoglobin. Sato-Tomita, A., Ang, A.K.R., Kimura, K. et al. Biochem Biophys Res Commun (2022) 635:277-282. DOI 10.1016/j.bbrc.2022.10.003 · 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
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

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