3CKD: PDB entry 3CKD

Name: PDB 3CKD: Crystal structure of the C-terminal domain of the Shigella type III effector IpaH
Published: 2008-03-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of the C-terminal domain of the Shigella type III effector IpaH. Determined by X-ray diffraction at 2.65 Å resolution. Released 25 Mar 2008.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Shigella flexneri 2a str. 301
Chains: 3
Atoms: 6,327
Mol. weight: 107.5 kDa
Released: 25 Mar 2008

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

Secondary structure: helices and β-sheets

3CKD contains 37 α-helices and 0 β-strands across 3 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: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	285-290	6
α-helix	306-308	3
α-helix	314-325	12
α-helix	336-349	14
α-helix	351-363	13
α-helix	372-390	19
α-helix	397-421	25
α-helix	429-439	11
α-helix	463-485	23
α-helix	489-497	9
α-helix	500-526	27
α-helix	535-564	30

Chain B: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	286-290	5
α-helix	314-324	11
α-helix	339-349	11
α-helix	351-361	11
α-helix	374-390	17
α-helix	397-420	24
α-helix	430-444	15
α-helix	463-485	23
α-helix	489-498	10
α-helix	500-529	30
α-helix	535-563	29

Chain C: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	285-290	6
α-helix	295-297	3
α-helix	298-306	9
α-helix	314-325	12
α-helix	334-349	16
α-helix	351-363	13
α-helix	372-390	19
α-helix	397-423	27
α-helix	429-439	11
α-helix	441-444	4
α-helix	463-486	24
α-helix	489-498	10
α-helix	500-529	30
α-helix	535-562	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery	A, B, C	protein	312	Shigella flexneri 2a str. 301	P18014 (AlphaFold model)

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

>3CKD_1 Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery (chains A, B, C)
GGPQIFFSMGNSATISAPEHSLADAVTAWFPENKQSDVSQIWHAFEHEEHANTFSAFLDR
LSDTVSARNTSGFREQVAAWLEKLSASAELRQQSFAVAADATESCEDRVALTWNNLRKTL
LVHQASEGLFDNDTGALLSLGREMFRLEILEDIARDKVRTLHFVDEIEVYLAFQTMLAEK
LQLSTAVKEMRFYGVSGVTANDLRTAEAMVRSREENEFTDWFSLWGPWHAVLKRTEADRW
AQAEEQKYEMLENEYSQRVADRLKASGLSGDADAEREAGAQVMRETEQQIYRQLTDEVLA
LRLSENGSNHIA

Primary citation

Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases. Singer, A.U., Rohde, J.R., Lam, R. et al. Nat Struct Mol Biol (2008) 15:1293-1301. DOI 10.1038/nsmb.1511 · PubMed

Other PDB entries of the same protein (UniProt P18014 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7WJQ 2.7 Å, Crystal structure of GSDMB in complex with Ipah7.8
8GTJ 2.7 Å, Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex
8GTK 3.1 Å, Crystal structure of IpaH7.8-LRR and GSDMB isoform-1 complex
8EFP 3.8 Å, CryoEM structure of GSDMB in complex with shigella IpaH7.8

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