6B7Q: SdeA

Crystal structure of Legionella effector protein sdeA (lpg2157) aa. 211-910. Determined by X-ray diffraction at 2.2 Å resolution. Released 18 Apr 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Legionella pneumophila
Chains: 1
Atoms: 5,518
Mol. weight: 81.97 kDa
Ligands: HG
Released: 18 Apr 2018

Explore 6B7Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B7Q contains 44 α-helices and 27 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: 44 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	227-229	3
α-helix	238-247	10
α-helix	248-252	5
α-helix	255-256	2
β-strand	265-267	3	1
β-strand	270-272	3	1
α-helix	279-301	23
α-helix	315-317	3
α-helix	320-332	13
α-helix	344-363	20
α-helix	366-373	8
α-helix	377-388	12
α-helix	391-393	3
α-helix	398-409	12
α-helix	410-413	4
α-helix	418-433	16
α-helix	435-451	17
β-strand	459-460	2	2
β-strand	466	1	3
α-helix	467	1
β-strand	469	1	4
β-strand	474	1	4
β-strand	475-476	2	5
β-strand	477-478	2	6
β-strand	484	1	6
β-strand	486	1	7
α-helix	489-490	2
α-helix	496-497	2
β-strand	498	1	7
α-helix	499	1
β-strand	500-501	2	5
α-helix	505-507	3
β-strand	512-513	2	6
α-helix	514	1
β-strand	515	1	3
α-helix	516-521	6
α-helix	523-526	4
β-strand	535-536	2	2
α-helix	545-552	8
α-helix	555-560	6
α-helix	564-585	22
α-helix	588-590	3
α-helix	592-594	3
α-helix	596-599	4
α-helix	600-614	15
α-helix	616-618	3
β-strand	619-620	2	8
β-strand	623-625	3	8
β-strand	630-631	2	8
α-helix	633-642	10
α-helix	645-650	6
α-helix	654-666	13
β-strand	671-672	2	9
α-helix	680-681	2
β-strand	682-683	2	9
α-helix	684-695	12
α-helix	701-714	14
α-helix	716-726	11
α-helix	735-755	21
α-helix	758-761	4
β-strand	763-768	6	10
α-helix	772-786	15
α-helix	809-815	7
β-strand	818-822	5	10
α-helix	825-826	2
α-helix	827-831	5
β-strand	836-841	6	10
β-strand	848-850	3	10
β-strand	862-866	5	10
β-strand	871-883	13	10
β-strand	889-899	11	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SdeA	A	protein	705	Legionella pneumophila	Q5ZTK4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6B7Q_1 SdeA (chains A)
GKDTSPKEMSVKPTAPQDKSVPVWNGFSLYTDDTVKAAAQYAYDNYLGKPYTGSVESAPA
NFGGRMVYRQHHGLSHTLRTMAYAELIVEEARKAKLRGETLGKFKDGRTIADVTPQELKK
IMIAQAFFVAGRDDEASDAKNYQKYHEQSRDAFLKYVKDNESTLLPDVFKDQEDVNFYAR
VIEDKSHDWESTPAHVLINQGHMVDLVRVKQPPESFLQRYFSSMQRWIGSQATEAVFGIQ
RQFFHATYEVVAGFDSDNKEPHLVVSGLGRYVIGEDGQPIREAPKKGQKEGDLKVFPQTY
KLKENERLMRVDEFLKLPEIQNTFPGSGKHLQGGMPGMNEMDYWNRLNSLNRARCENDVD
FCLKQLQTAHDKAKIEPIKQAFQSSKGKERRQPNVDEIAAARIIQQILANPDCIHDDHVL
INGQKLEQQFFRDLLAKCEMAVVGSLLNDTDIGNIDTLMRHEKDTEFHSTNPEAVPVKIG
EYWINDQRINNSSGNITQKKHDLIFLMQNDAWYFSRVNAIAQNRDKGSTFKEVLITTLMT
PLTSKALVDTSQAKPPTRLFRGLNLSEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQI
KLNDLSKMSGRTNASTTTEIKLVKETWDSNVIFEMLDPDGLLHSKQVGRHGEGTESEFSV
YLPEDVALVPVKVTLDGKTQKGENRYVFTFVAVKSPDFTPRHESG

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	10

Primary citation

Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector. Akturk, A., Wasilko, D.J., Wu, X. et al. Nature (2018) 557:729-733. DOI 10.1038/s41586-018-0147-6 · 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
5YSJ 2.06 Å, SdeA mART-C domain WT apo
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 6B7Q 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.