5YSJ: SdeA mART-C domain WT apo

SdeA mART-C domain WT apo. Determined by X-ray diffraction at 2.06 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Legionella pneumophila subsp. pneumophila
Chains: 4
Atoms: 4,476
Mol. weight: 67.6 kDa
Released: 29 Aug 2018

Explore 5YSJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YSJ contains 19 α-helices and 28 β-strands across 4 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	763-768	6	1
α-helix	772-787	16
α-helix	789-796	8
α-helix	799-808	10
β-strand	819-822	4	1
α-helix	825-831	7
β-strand	836-841	6	1
β-strand	850-851	2	1
β-strand	862-865	4	1
β-strand	871-883	13	1
β-strand	889-899	11	1

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	763-768	6	2
α-helix	772-787	16
α-helix	789-794	6
α-helix	799-808	10
β-strand	819-822	4	2
α-helix	825-831	7
β-strand	836-841	6	2
β-strand	848-851	4	2
β-strand	862-866	5	2
β-strand	871-883	13	2
β-strand	889-899	11	2

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	763-768	6	3
α-helix	772-787	16
α-helix	789-794	6
α-helix	799-808	10
β-strand	819-822	4	3
α-helix	825-831	7
β-strand	836-841	6	3
β-strand	850-851	2	3
β-strand	862-865	4	3
β-strand	871-883	13	3
β-strand	889-899	11	3
α-helix	900-901	2

Chain D: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	763-768	6	4
α-helix	772-787	16
α-helix	789-794	6
α-helix	799-808	10
β-strand	819-822	4	4
α-helix	825-831	7
β-strand	836-841	6	4
β-strand	850-851	2	4
α-helix	855-857	3
β-strand	862-865	4	4
β-strand	871-883	13	4
β-strand	889-899	11	4
α-helix	900-901	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitinating/deubiquitinating enzyme SdeA	A, B, C, D	protein	152	Legionella pneumophila subsp. pneumophila	Q5ZTK4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5YSJ_1 Ubiquitinating/deubiquitinating enzyme SdeA (chains A, B, C, D)
GSSQAKPPTRLFRGLNLSEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLSKM
SGRTNASTTTEIKLVKETWDSNVIFEMLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVAL
VPVKVTLDGKTQKGENRYVFTFVAVKSPDFTP

Primary citation

Structural and Biochemical Study of the Mono-ADP-Ribosyltransferase Domain of SdeA, a Ubiquitylating/Deubiquitylating Enzyme from Legionella pneumophila. Kim, L., Kwon, D.H., Kim, B.H. et al. J Mol Biol (2018) 430:2843-2856. DOI 10.1016/j.jmb.2018.05.043 · PubMed

Other PDB entries of the same protein (UniProt Q5ZTK4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YSI 1.55 Å, SdeA mART-C domain EE/AA NCA complex
9R3T 1.98 Å, C-terminal domain of SdeA Legionella effector
6B7Q 2.2 Å, Crystal structure of Legionella effector protein sdeA (lpg2157) aa. 211-910
5YSK 2.4 Å, SdeA mART-C domain EE/AA apo
7MIR 2.5 Å, Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex
6WTG 2.63 Å, SdeA DUB Domain in complex with Ubiquitin
6G0C 2.8 Å, Crystal structure of SdeA catalytic core
8EFW 2.81 Å, Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin
7PPO 2.91 Å, Structure of SidJ/CaM bound to SdeA in pre-glutamylation state
7PQE 3.7 Å, Structure of SidJ/CaM bound to SdeA in post-catalysis state

Browse structure collections

About this viewer

MolViewer shows 5YSJ 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.