5LI1: Par3-inhibitory peptide

Structure of a Par3-inhibitory peptide bound to PKCiota core kinase domain. Determined by X-ray diffraction at 2.0 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, Xenopus tropicalis
Chains: 2
Atoms: 3,109
Mol. weight: 43.99 kDa
Ligands: MG, ANP
Released: 14 Sept 2016

Explore 5LI1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LI1 contains 19 α-helices and 16 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: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	251-253	3
β-strand	254-262	9	1
β-strand	267-273	7	1
β-strand	278-286	9	1
α-helix	287-289	3
α-helix	293-309	17
β-strand	315	1	2
β-strand	318-323	6	1
β-strand	327-332	6	1
β-strand	339	1	2
α-helix	340-347	8
α-helix	352-371	20
β-strand	375	1	3
α-helix	381-383	3
β-strand	384-386	3	2
β-strand	392-394	3	2
β-strand	401	1	3
β-strand	410	1	4
β-strand	414-415	2	5
α-helix	417-419	3
α-helix	422-425	4
β-strand	430	1	4
α-helix	433-448	16
α-helix	467-476	10
α-helix	487-496	10
α-helix	512-517	6
α-helix	520-522	3
α-helix	527-530	4
α-helix	546-551	6
α-helix	554-557	4
α-helix	563-566	4
α-helix	568-571	4
α-helix	576-579	4
β-strand	584-585	2	1

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	13-14	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein kinase C iota type	A	protein	354	Homo sapiens	P41743 (AlphaFold model)
Par-3 partitioning defective 3 homolog (C. elegans)	B	protein	20	Xenopus tropicalis	Q28E03 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5LI1_1 Protein kinase C iota type (chains A)
GPLSFSLGLQDFDLLRVIGRGSYAKVLLVRLKKTDRIYAMKVVKKELVNDDEDIDWVQTE
KHVFEQASNHPFLVGLHSCFQTESRLFFVIEYVNGGDLMFHMQRQRKLPEEHARFYSAEI
SLALNYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLRPGDTTSTFCGTPNYIAP
EILRGEDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNPDQNTEDYLFQVILEKQIRIP
RSLSVKAASVLKSFLNKDPKERLGCHPQTGFADIQGHPFFRNVDWDMMEQKQVVPPFKPN
ISGEFGLDNFDSQFTNEPVQLTPDDDDIVRKIDQSEFEGFEYINPLLMSAEECV

Sequence of entity 2 (B), FASTA

>5LI1_2 Par-3 partitioning defective 3 homolog (C. elegans) (chains B)
LAFQREGFGRQSMSEKRTKQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Water and common crystallization additives (K, GOL) are not listed.

Primary citation

aPKC Inhibition by Par3 CR3 Flanking Regions Controls Substrate Access and Underpins Apical-Junctional Polarization. Soriano, E.V., Ivanova, M.E., Fletcher, G. et al. Dev Cell (2016) 38:384-398. DOI 10.1016/j.devcel.2016.07.018 · PubMed

Other PDB entries of the same protein (UniProt P41743 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WMH 1.5 Å, Crystal structure of a PB1 domain complex of Protein kinase c iota and Par6 alpha
5LI9 1.79 Å, Structure of a nucleotide-bound form of PKCiota core kinase domain
3A8X 2.0 Å, Crystal Structure of PKCiota kinase domain
3A8W 2.1 Å, Crystal Structure of PKCiota kinase domain
8R3X 2.59 Å, Crystal structure of aPKC Iota kinase domain with LLGL2 peptide
3ZH8 2.74 Å, A novel small molecule aPKC inhibitor
1ZRZ 3.0 Å, Crystal Structure of the Catalytic Domain of Atypical Protein Kinase C-iota
9EJK 3.08 Å, Lgl2 bound to the aPKCiota-Par6b complex in nucleotide-free form. Head sub-complex…
5LIH 3.25 Å, Structure of a peptide-substrate bound to PKCiota core kinase domain
6ILZ 3.26 Å, Crystal structure of PKCiota in complex with inhibitor
9EJM 3.33 Å, Lgl2 bound to the aPKCiota-Par6B complex in its ADP-bound form
9EJL 3.48 Å, Lgl2 bound to the aPKCiota-Par6B complex in nucleotide-free form. Conformation with…

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