6ILZ: PKCiota

Crystal structure of PKCiota in complex with inhibitor. Determined by X-ray diffraction at 3.26 Å resolution. Released 26 Jun 2019.

Method: X-ray diffraction
Resolution: 3.26 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,673
Mol. weight: 160.92 kDa
Ligands: AFU
Released: 26 Jun 2019

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

Secondary structure: helices and β-sheets

6ILZ contains 54 α-helices and 53 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: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	255-262	8	1
β-strand	266-272	7	1
β-strand	279-286	8	1
α-helix	287-290	4
α-helix	297-309	13
β-strand	315	1	2
β-strand	318-323	6	1
β-strand	327-333	7	1
β-strand	338-339	2	2
α-helix	340-346	7
α-helix	352-372	21
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
α-helix	422-425	4
β-strand	430	1	4
α-helix	433-448	16
α-helix	469-476	8
α-helix	487-496	10
α-helix	512-517	6
α-helix	527-531	5
α-helix	536-537	2
α-helix	540-542	3
α-helix	563-566	4
α-helix	568-573	6

Chain C: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	256-262	7	5
β-strand	266-271	6	5
β-strand	280-286	7	5
α-helix	288-291	4
α-helix	296-309	14
β-strand	315	1	6
β-strand	318-323	6	5
β-strand	327-333	7	5
β-strand	338-339	2	6
α-helix	340-346	7
α-helix	352-372	21
β-strand	374-375	2	7
β-strand	384-386	3	6
β-strand	392-394	3	6
β-strand	401-402	2	7
β-strand	410	1	8
α-helix	422-426	5
β-strand	430	1	8
α-helix	434-448	15
α-helix	470-476	7
α-helix	487-496	10
α-helix	512-517	6
α-helix	527-531	5
α-helix	536-537	2
α-helix	562-565	4
α-helix	568-573	6

Chain E: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	259	1	9
β-strand	266-271	6	9
β-strand	280-286	7	9
α-helix	287-291	5
α-helix	297-310	14
β-strand	315	1	10
β-strand	318-323	6	9
β-strand	327-332	6	9
β-strand	338-339	2	10
α-helix	340-346	7
α-helix	352-372	21
β-strand	374-375	2	11
β-strand	384-386	3	10
β-strand	392-394	3	10
β-strand	401-402	2	11
β-strand	410	1	12
α-helix	422-426	5
β-strand	430	1	12
α-helix	433-448	16
α-helix	468-476	9
α-helix	487-496	10
α-helix	512-518	7
α-helix	527-531	5
α-helix	540-542	3
α-helix	563-565	3
α-helix	568-571	4

Chain G: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	255	1	13
β-strand	259-262	4	14
β-strand	267-271	5	14
β-strand	272	1	13
β-strand	280-286	7	14
α-helix	288-291	4
α-helix	297-309	13
β-strand	315	1	15
β-strand	318-323	6	14
β-strand	327-332	6	14
β-strand	338-339	2	16
α-helix	340-346	7
α-helix	352-372	21
β-strand	374-375	2	17
β-strand	385-386	2	16
β-strand	392-393	2	16
β-strand	394	1	15
β-strand	401-402	2	17
α-helix	422-426	5
α-helix	434-448	15
α-helix	469-476	8
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	548-550	3
α-helix	568-571	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein kinase C iota type	A, C, E, G	protein	345	Homo sapiens	P41743 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>6ILZ_1 Protein kinase C iota type (chains A, C, E, G)
GAMDPLGLQDFDLLRVIGRGSYAKVLLVRLKKTDRIYAMKVVKKELVNDDEDIDWVQTEK
HVFEQASNHPFLVGLHSCFQTESRLFFVIEYVNGGDLMFHMQRQRKLPEEHARFYSAEIS
LALNYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLRPGDTTSTFCGTPNYIAPE
ILRGEDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNPDQNTEDYLFQVILEKQIRIPR
SLSVKAASVLKSFLNKDPKERLGCHPQTGFADIQGHPFFRNVDWDMMEQKQVVPPFKPNI
SGEFGLDNFDSQFTNEPVQLTPDDDDIVRKIDQSEFEGFEYINPL

Ligands and cofactors

ID	Name	Formula	Copies
AFU	2-amino-5-[3-(piperazin-1-yl)phenyl]-N-(pyridin-4-yl)pyridine-3-carboxamide	C21 H22 N6 O	4

Primary citation

Fragment-based Discovery of a Small-Molecule Protein Kinase C-iota Inhibitor Binding Post-kinase Domain Residues. Kwiatkowski, J., Baburajendran, N., Poulsen, A. et al. ACS Med Chem Lett (2019) 10:318-323. DOI 10.1021/acsmedchemlett.8b00546 · 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…
5LIH 3.25 Å, Structure of a peptide-substrate bound to PKCiota core kinase domain
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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