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- PDB-6ilz: Crystal structure of PKCiota in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6ilz
TitleCrystal structure of PKCiota in complex with inhibitor
ComponentsProtein kinase C iota type
KeywordsTRANSFERASE / Kinase / Atypical kinase / phosphorylation / inhibitor / PKCiota / iota type / kinase domain
Function / homology
Function and homology information


Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / negative regulation of glial cell apoptotic process / eye photoreceptor cell development / diacylglycerol-dependent serine/threonine kinase activity / Schmidt-Lanterman incisure / cellular response to chemical stress ...Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / negative regulation of glial cell apoptotic process / eye photoreceptor cell development / diacylglycerol-dependent serine/threonine kinase activity / Schmidt-Lanterman incisure / cellular response to chemical stress / membrane organization / positive regulation of endothelial cell apoptotic process / cell-cell junction organization / tight junction / establishment or maintenance of epithelial cell apical/basal polarity / protein targeting to membrane / intercellular bridge / positive regulation of Notch signaling pathway / cell leading edge / regulation of postsynaptic membrane neurotransmitter receptor levels / brush border / bicellular tight junction / vesicle-mediated transport / positive regulation of glial cell proliferation / cytoskeleton organization / p75NTR recruits signalling complexes / response to interleukin-1 / secretion / positive regulation of glucose import / positive regulation of protein localization to plasma membrane / actin filament organization / Schaffer collateral - CA1 synapse / phospholipid binding / Pre-NOTCH Transcription and Translation / positive regulation of neuron projection development / cellular response to insulin stimulus / microtubule cytoskeleton / KEAP1-NFE2L2 pathway / cell migration / positive regulation of NF-kappaB transcription factor activity / negative regulation of neuron apoptotic process / protein kinase activity / intracellular signal transduction / endosome / apical plasma membrane / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding ...Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AFU / Protein kinase C iota type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.261 Å
AuthorsBaburajendran, N. / Hill, J.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Fragment-based Discovery of a Small-Molecule Protein Kinase C-iota Inhibitor Binding Post-kinase Domain Residues.
Authors: Kwiatkowski, J. / Baburajendran, N. / Poulsen, A. / Liu, B. / Tee, D.H.Y. / Wong, Y.X. / Poh, Z.Y. / Ong, E.H. / Dinie, N. / Cherian, J. / Jansson, A.E. / Hill, J. / Keller, T.H. / Hung, A.W.
History
DepositionOct 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C iota type
C: Protein kinase C iota type
E: Protein kinase C iota type
G: Protein kinase C iota type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,9178
Polymers159,4194
Non-polymers1,4984
Water00
1
A: Protein kinase C iota type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2292
Polymers39,8551
Non-polymers3741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein kinase C iota type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2292
Polymers39,8551
Non-polymers3741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Protein kinase C iota type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2292
Polymers39,8551
Non-polymers3741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Protein kinase C iota type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2292
Polymers39,8551
Non-polymers3741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.870, 87.630, 105.181
Angle α, β, γ (deg.)90.000, 114.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein kinase C iota type / Atypical protein kinase C-lambda/iota / aPKC-lambda/iota / nPKC-iota


Mass: 39854.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCI, DXS1179E / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41743, protein kinase C
#2: Chemical
ChemComp-AFU / 2-amino-5-[3-(piperazin-1-yl)phenyl]-N-(pyridin-4-yl)pyridine-3-carboxamide


Mass: 374.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22N6O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS 6.5, 28 % w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.261→51.579 Å / Num. obs: 22181 / % possible obs: 97.23 % / Redundancy: 2 % / CC1/2: 0.947 / Rmerge(I) obs: 0.08004 / Rpim(I) all: 0.08004 / Rrim(I) all: 0.1132 / Net I/σ(I): 9.71
Reflection shellResolution: 3.261→3.378 Å / Rmerge(I) obs: 0.1936 / Num. unique obs: 22181 / CC1/2: 0.803 / Rpim(I) all: 0.1936 / Rrim(I) all: 0.2737

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A8W

3a8w


Resolution: 3.261→51.579 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 34.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3477 1994 9 %
Rwork0.3057 20157 -
obs0.3096 22151 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.42 Å2 / Biso mean: 32.564 Å2 / Biso min: 21.63 Å2
Refinement stepCycle: final / Resolution: 3.261→51.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9561 0 112 0 9673
Biso mean--31.58 --
Num. residues----1268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.261-3.34260.37871310.37761311144291
3.3426-3.43290.43541360.38021390152695
3.4329-3.53390.44041400.39011424156497
3.5339-3.6480.40621440.34421478162298
3.648-3.77830.38371420.33841432157498
3.7783-3.92950.34561420.32081448159098
3.9295-4.10830.41921410.30661419156098
4.1083-4.32480.35211450.2911441158698
4.3248-4.59560.28281470.28241474162198
4.5956-4.95020.31881430.26211449159298
4.9502-5.44790.30761470.28421480162798
5.4479-6.2350.35321460.30511454160098
6.235-7.8510.31911470.27621463161098
7.851-51.58570.29091430.26141494163797
Refinement TLS params.Method: refined / Origin x: 55.2372 Å / Origin y: 0.784 Å / Origin z: 68.1343 Å
111213212223313233
T0.2526 Å20.0503 Å20.0489 Å2-0.3457 Å20.0039 Å2--0.2436 Å2
L0.5801 °20.0514 °20.1623 °2-0.1787 °20.0012 °2--0.2678 °2
S0.0446 Å °-0.1593 Å °-0.0153 Å °-0.0601 Å °0.0201 Å °-0.006 Å °0.0784 Å °-0.0499 Å °-0.0619 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA254 - 587
2X-RAY DIFFRACTION1allB2
3X-RAY DIFFRACTION1allC254 - 587
4X-RAY DIFFRACTION1allD2
5X-RAY DIFFRACTION1allE255 - 587
6X-RAY DIFFRACTION1allF2
7X-RAY DIFFRACTION1allG254 - 587
8X-RAY DIFFRACTION1allH2

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