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- PDB-4oth: Crystal Structure of PRK1 Catalytic Domain in Complex with Ro-31-8220 -

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Basic information

Entry
Database: PDB / ID: 4oth
TitleCrystal Structure of PRK1 Catalytic Domain in Complex with Ro-31-8220
ComponentsSerine/threonine-protein kinase N1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PRK1 / PKN1 / Protein kinase C related kinase 1 / KINASE / PROTEIN KINASE / ATP BINDING / PHOSPHORYLATION / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


epithelial cell migration / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / renal system process / regulation of germinal center formation / B cell apoptotic process / histone H3T11 kinase activity / hyperosmotic response / regulation of cell motility / regulation of androgen receptor signaling pathway ...epithelial cell migration / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / renal system process / regulation of germinal center formation / B cell apoptotic process / histone H3T11 kinase activity / hyperosmotic response / regulation of cell motility / regulation of androgen receptor signaling pathway / regulation of immunoglobulin production / nuclear androgen receptor binding / RHOB GTPase cycle / RHOC GTPase cycle / negative regulation of B cell proliferation / cleavage furrow / B cell homeostasis / RHOA GTPase cycle / RHO GTPases activate PKNs / spleen development / RAC1 GTPase cycle / post-translational protein modification / protein kinase C binding / nuclear receptor coactivator activity / negative regulation of protein phosphorylation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / small GTPase binding / histone deacetylase binding / midbody / histone binding / endosome / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase N1, second HR1 domain / Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain ...Serine/threonine-protein kinase N1, second HR1 domain / Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / C2 domain / C2 domain profile. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / 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
BISINDOLYLMALEIMIDE IX / Serine/threonine-protein kinase N1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChamberlain, P.P. / Delker, S. / Pagarigan, B. / Mahmoudi, A. / Jackson, P. / Abbassian, M. / Muir, J. / Raheja, N. / Cathers, B.
CitationJournal: Plos One / Year: 2014
Title: Crystal Structures of PRK1 in Complex with the Clinical Compounds Lestaurtinib and Tofacitinib Reveal Ligand Induced Conformational Changes.
Authors: Chamberlain, P. / Delker, S. / Pagarigan, B. / Mahmoudi, A. / Jackson, P. / Abbasian, M. / Muir, J. / Raheja, N. / Cathers, B.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7992
Polymers38,3421
Non-polymers4581
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.319, 72.197, 94.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase N1 / Protease-activated kinase 1 / PAK-1 / Protein kinase C-like 1 / Protein kinase C-like PKN / Protein ...Protease-activated kinase 1 / PAK-1 / Protein kinase C-like 1 / Protein kinase C-like PKN / Protein kinase PKN-alpha / Protein-kinase C-related kinase 1 / Serine-threonine protein kinase N


Mass: 38341.504 Da / Num. of mol.: 1 / Fragment: UNP residues 605-942
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKN1, PAK1, PKN, PRK1, PRKCL1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16512, protein kinase C
#2: Chemical ChemComp-DRN / BISINDOLYLMALEIMIDE IX / Ro-318220


Mass: 457.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23N5O2S / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: 100mM Tris pH 8.5, 150-225mM Ammonium acetate, 23-28% PEG 3350, Vapor diffusion

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33917 / % possible obs: 92.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.043 / Χ2: 1.297 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.832.40.29515110.586184.1
1.83-1.862.50.25216150.626190.4
1.86-1.92.50.48716170.791190.7
1.9-1.942.30.15712893.909171
1.94-1.983.60.22717780.994199.9
1.98-2.033.60.13618040.786199.7
2.03-2.083.60.11318100.85199.9
2.08-2.133.60.09818000.8941100
2.13-2.23.60.08518060.9251100
2.2-2.272.60.1089491.568152.2
2.27-2.353.50.0716941.116193.7
2.35-2.443.60.05318140.959199.9
2.44-2.553.60.04618220.9711100
2.55-2.693.60.04118370.9951100
2.69-2.863.60.03818031.138199.9
2.86-3.083.60.03518381.3231100
3.08-3.393.60.04118522.103199.9
3.39-3.883.10.04415953.209186
3.88-4.883.30.03817062.874190.5
4.88-503.30.02219771.062198.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.32 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1653 5 %RANDOM
Rwork0.2009 ---
obs0.2041 33191 90.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 29.687 Å2 / Biso min: 8.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 33 302 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222555
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.973466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25822.623122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68415.035424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6691525
X-RAY DIFFRACTIONr_chiral_restr0.1090.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021972
X-RAY DIFFRACTIONr_nbd_refined0.2050.21190
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21736
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.220
X-RAY DIFFRACTIONr_mcbond_it2.12531581
X-RAY DIFFRACTIONr_mcangle_it2.82842468
X-RAY DIFFRACTIONr_scbond_it3.17841111
X-RAY DIFFRACTIONr_scangle_it4.3155995
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 97 -
Rwork0.285 2140 -
all-2237 -
obs--84.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7336-0.4431-0.57920.87170.62311.42040.021-0.0313-0.0050.0053-0.00380.03420.04110.0029-0.0172-0.0486-0.0167-0.0121-0.0441-0.0297-0.0381-11.495210.3157-2.9642
20.9-0.217-0.05511.0474-0.11280.93110.05060.0593-0.06530.0489-0.06020.09090.0561-0.0190.0096-0.0498-0.02770.0059-0.0465-0.0439-0.0634-25.9312-3.5635-21.0642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A612 - 704
2X-RAY DIFFRACTION1A907 - 944
3X-RAY DIFFRACTION2A705 - 906

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