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- PDB-5zjw: Crystal Structure of PAK4 in complex with inhibitor CZg353 -

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Basic information

Entry
Database: PDB / ID: 5zjw
TitleCrystal Structure of PAK4 in complex with inhibitor CZg353
ComponentsSerine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / ATP binding pocket
Function / homology
Function and homology information


dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / RAC1 GTPase cycle / cytoskeleton organization / cellular response to starvation / adherens junction / regulation of cell growth / positive regulation of angiogenesis / cell migration / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / cytosol / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase 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-9EO / BICARBONATE ION / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.798 Å
AuthorsZhao, F. / Li, H.
CitationJournal: To be published
Title: Crystal Structure of PAK4 in complex with inhibitor CZg353
Authors: Zhao, F. / Li, H.
History
DepositionMar 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,22912
Polymers33,0981
Non-polymers1,13011
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint26 kcal/mol
Surface area13390 Å2
Unit cell
Length a, b, c (Å)43.117, 63.399, 100.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 33098.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Plasmid: pSUMOH10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O96013, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 294 molecules

#2: Chemical ChemComp-9EO / (3Z)-N-[(1S)-2-hydroxy-1-phenylethyl]-3-[(1H-imidazol-2-yl)(phenyl)methylidene]-2-oxo-2,3-dihydro-1H-indole-5-carboxamide


Mass: 450.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H22N4O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.68 % / Mosaicity: 0.316 ° / Mosaicity esd: 0.006 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M Bis-tris pH 6.5, 25% PEG 3350, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2018 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26329 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.059 / Rrim(I) all: 0.152 / Χ2: 0.845 / Net I/σ(I): 3.4 / Num. measured all: 172803
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.70.79512720.7180.330.8620.49100
1.83-1.866.80.73813020.830.3040.7990.49299.8
1.86-1.96.70.61612660.830.2550.6680.516100
1.9-1.946.70.53513020.8740.2220.580.544100
1.94-1.986.70.44813070.9210.1870.4860.587100
1.98-2.036.40.40212860.9040.1710.4370.598100
2.03-2.086.20.33613000.9170.1470.3680.66999.8
2.08-2.136.80.31613060.9450.130.3420.71100
2.13-2.26.80.28313000.9440.1160.3060.753100
2.2-2.276.80.2513120.9540.1030.2710.79799.9
2.27-2.356.70.22512900.9560.0940.2440.869100
2.35-2.446.50.20913140.9590.0890.2270.903100
2.44-2.556.20.1913090.9660.0830.2070.95899.9
2.55-2.696.90.1713140.9740.070.1840.959100
2.69-2.866.70.15313140.9740.0640.1661.035100
2.86-3.086.60.13713500.9810.0570.1491.112100
3.08-3.396.20.1213150.9820.0520.1311.233100
3.39-3.886.70.10513450.9890.0440.1141.347100
3.88-4.886.20.09413730.990.0410.1021.42499.9
4.88-506.10.07814520.9910.0340.0860.90499.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 1.798→39.364 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 1279 4.87 %
Rwork0.1682 24980 -
obs0.1705 26259 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.96 Å2 / Biso mean: 23.9068 Å2 / Biso min: 10.78 Å2
Refinement stepCycle: final / Resolution: 1.798→39.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 78 283 2681
Biso mean--28.87 33.64 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062446
X-RAY DIFFRACTIONf_angle_d0.9293299
X-RAY DIFFRACTIONf_chiral_restr0.054365
X-RAY DIFFRACTIONf_plane_restr0.005420
X-RAY DIFFRACTIONf_dihedral_angle_d14.2941490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7984-1.87040.29361420.22822715285799
1.8704-1.95550.26791570.199826982855100
1.9555-2.05860.23051390.181127372876100
2.0586-2.18760.22541230.164427752898100
2.1876-2.35640.2451570.165827142871100
2.3564-2.59350.22231380.172327662904100
2.5935-2.96870.23531530.168427852938100
2.9687-3.73980.19261380.156428292967100
3.7398-39.37350.18181320.161829613093100

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