3EKE: IBV X-domain at pH 5.6

Crystal structure of IBV X-domain at pH 5.6. Determined by X-ray diffraction at 2.1 Å resolution. Released 30 Sept 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Avian infectious bronchitis virus (strain Beaudette)
Chains: 1
Atoms: 1,430
Mol. weight: 19.72 kDa
Ligands: TLA
Released: 30 Sept 2008

Explore 3EKE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EKE contains 8 α-helices and 6 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	11-16	6	1
α-helix	19-29	11
β-strand	33-38	6	1
α-helix	48-57	10
α-helix	59-72	14
β-strand	77-80	4	1
β-strand	87-93	7	1
α-helix	103-112	10
β-strand	121-125	5	1
α-helix	126-128	3
α-helix	136-147	12
β-strand	153-158	6	1
α-helix	161-170	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 3	A	protein	176	Avian infectious bronchitis virus (strain Beaudette)	P0C6Y1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3EKE_1 Non-structural protein 3 (chains A)
GAMAPATCEKPKFLEYKTCVGDLTVVIAKALDEFKEFCIVNAANEHMTHGSGVAKAIADF
CGLDFVEYCEDYVKKHGPQQRLVTPSFVKGIQCVNNVVGPRHGDNNLHEKLVAAYKNVLV
DGVVNYVVPVLSLGIFGVDFKMSIDAMREAFEGCTIRVLLFSLSQEHIDYFDVTCK

Ligands and cofactors

ID	Name	Formula	Copies
TLA	L(+)-tartaric acid	C4 H6 O6	2

Primary citation

Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property. Piotrowski, Y., Hansen, G., Boomaars-van der Zanden, A.L. et al. Protein Sci (2009) 18:6-16. DOI 10.1002/pro.15 · PubMed

Other PDB entries of the same protein (UniProt P0C6Y1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EJF 1.6 Å, Crystal structure of IBV X-domain at pH 8.5
5BZ0 2.1 Å, Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin
4X2Z 2.15 Å, Structural view and substrate specificity of papain-like protease from Avian Infectious…

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