2DC3: Human cytoglobin

Crystal structure of human cytoglobin at 1.68 angstroms resolution. Determined by X-ray diffraction at 1.68 Å resolution. Released 23 May 2006.

Method: X-ray diffraction
Resolution: 1.68 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,126
Mol. weight: 44.72 kDa
Ligands: HEM
Released: 23 May 2006

Explore 2DC3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2DC3 contains 21 α-helices and 0 β-strands across 2 chains. 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	18-20	3
α-helix	21-35	15
α-helix	38-52	15
α-helix	54-59	6
α-helix	69-72	4
α-helix	76-94	19
α-helix	99-115	17
α-helix	121-138	18
α-helix	140-142	3
α-helix	145-168	24
α-helix	181-183	3

Chain B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	7-15	9
α-helix	19-20	2
α-helix	21-35	15
α-helix	38-52	15
α-helix	54-59	6
α-helix	69-74	6
α-helix	76-94	19
α-helix	99-115	17
α-helix	122-138	17
α-helix	145-168	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoglobin	A, B	protein	193	Homo sapiens	Q8WWM9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2DC3_1 Cytoglobin (chains A, B)
GSHMEKVPGEMEIERRERSEELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAK
QYFSQFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKH
KVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLIYSHVTAAYKEVGWVQQVPN
ATTPPATLPSSGP

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2

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

Primary citation

High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode. Makino, M., Sugimoto, H., Sawai, H. et al. Acta Crystallogr D Biol Crystallogr (2006) 62:671-677. DOI 10.1107/S0907444906013813 · PubMed

Other PDB entries of the same protein (UniProt Q8WWM9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1URV 2.0 Å, Crystal structure of cytoglobin: the fourth globin type discovered in man displays heme…
1UT0 2.1 Å, Crystal structure of cytoglobin: the fourth globin type discovered in man displays heme…
1URY 2.4 Å, cytoglobin cavities
1UX9 2.4 Å, Mapping protein matrix cavities in human cytoglobin through Xe atom binding: a…
1V5H 2.4 Å, Crystal Structure of Human Cytoglobin (Ferric Form)
1UMO 2.59 Å, The crystal structure of cytoglobin: the fourth globin type discovered in man
3AG0 2.6 Å, Crystal structure of carbonmonoxy human cytoglobin
4B3W 2.8 Å, Crystal structure of human cytoglobin H(E7)Q mutant

Browse structure collections

About this viewer

MolViewer shows 2DC3 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.