5LIH: Peptide-substrate

Structure of a peptide-substrate bound to PKCiota core kinase domain. Determined by X-ray diffraction at 3.25 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,298
Mol. weight: 86.38 kDa
Ligands: ADP, AF3, MN, SCN
Released: 14 Sept 2016

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

Secondary structure: helices and β-sheets

5LIH contains 37 α-helices and 32 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: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	251-253	3
β-strand	254-262	9	1
β-strand	266-273	8	1
β-strand	279-286	8	1
α-helix	301-309	9
β-strand	315	1	2
α-helix	316-317	2
β-strand	318-323	6	1
β-strand	327-332	6	1
β-strand	339	1	2
α-helix	342-345	4
α-helix	352-370	19
β-strand	375	1	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	422-425	4
β-strand	430	1	4
α-helix	433-448	16
α-helix	467-476	10
α-helix	478-479	2
α-helix	487-496	10
α-helix	512-518	7
α-helix	520-522	3
α-helix	527-531	5
α-helix	536-537	2
α-helix	546-551	6
α-helix	564-566	3
α-helix	571-573	3
α-helix	576-578	3
β-strand	584-585	2	1

Chain B: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	251-253	3
β-strand	254-262	9	6
β-strand	266-273	8	6
β-strand	279-286	8	6
α-helix	301-309	9
β-strand	315	1	7
α-helix	316-317	2
β-strand	318-323	6	6
β-strand	327-332	6	6
β-strand	339	1	7
α-helix	342-345	4
α-helix	352-370	19
β-strand	375	1	8
α-helix	381-383	3
β-strand	384-386	3	7
β-strand	392-394	3	7
β-strand	401	1	8
β-strand	410	1	9
β-strand	414-415	2	10
α-helix	422-425	4
β-strand	430	1	9
α-helix	433-448	16
α-helix	467-476	10
α-helix	478-479	2
α-helix	487-496	10
α-helix	512-518	7
α-helix	520-523	4
α-helix	527-531	5
α-helix	536-537	2
α-helix	546-551	6
α-helix	564-566	3
α-helix	571-573	3
α-helix	576-578	3
β-strand	584-585	2	6

Chains F and G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	12-13	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein kinase C iota type	A, B	protein	349	Homo sapiens	P41743 (AlphaFold model)
PKC Epsilon pseudo substrate sequence	F, G	protein	16	Homo sapiens	Q02156 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5LIH_1 Protein kinase C iota type (chains A, B)
SLGLQDFDLLRVIGRGSYAKVLLVRLKKTDRIYAMKVVKKELVNDDEDIDWVQTEKHVFE
QASNHPFLVGLHSCFQTESRLFFVIEYVNGGDLMFHMQRQRKLPEEHARFYSAEISLALN
YLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLRPGDTTSTFCGTPNYIAPEILRG
EDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNPDQNTEDYLFQVILEKQIRIPRSLSV
KAASVLKSFLNKDPKERLGCHPQTGFADIQGHPFFRNVDWDMMEQKQVVPPFKPNISGEF
GLDNFDSQFTNEPVQLTPDDDDIVRKIDQSEFEGFEYINPLLMSAEECV

Sequence of entity 2 (F, G), FASTA

>5LIH_2 PKC Epsilon pseudo substrate sequence (chains F, G)
ERMRPFKRQGSVRRRV

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
AF3	Aluminum fluoride	Al F3	4
MN	Manganese (II) ion	Mn	5
SCN	Thiocyanate ion	C N S	2

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
5LI1 2.0 Å, Structure of a Par3-inhibitory peptide bound to PKCiota core 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…
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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