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- PDB-9lbg: The crystal structure of the truncated PAK2 containing K278R mutant -

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Basic information

Entry
Database: PDB / ID: 9lbg
TitleThe crystal structure of the truncated PAK2 containing K278R mutant
ComponentsSerine/threonine-protein kinase PAK 2
KeywordsTRANSFERASE / inactive PAK2
Function / homology
Function and homology information


Regulation of PAK-2p34 activity by PS-GAP/RHG10 / protein localization to cell-cell junction / Stimulation of the cell death response by PAK-2p34 / dendritic spine development / bicellular tight junction assembly / cardiac muscle hypertrophy / Nef and signal transduction / adherens junction assembly / Activation of RAC1 / positive regulation of extrinsic apoptotic signaling pathway ...Regulation of PAK-2p34 activity by PS-GAP/RHG10 / protein localization to cell-cell junction / Stimulation of the cell death response by PAK-2p34 / dendritic spine development / bicellular tight junction assembly / cardiac muscle hypertrophy / Nef and signal transduction / adherens junction assembly / Activation of RAC1 / positive regulation of extrinsic apoptotic signaling pathway / Ephrin signaling / CD28 dependent Vav1 pathway / negative regulation of stress fiber assembly / regulation of axonogenesis / RHOV GTPase cycle / RHOJ GTPase cycle / regulation of cytoskeleton organization / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / protein tyrosine kinase activator activity / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / cellular response to transforming growth factor beta stimulus / negative regulation of protein kinase activity / Regulation of activated PAK-2p34 by proteasome mediated degradation / RAC1 GTPase cycle / CD209 (DC-SIGN) signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / secretory granule / cellular response to starvation / VEGFR2 mediated vascular permeability / MAPK6/MAPK4 signaling / FCERI mediated MAPK activation / small GTPase binding / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / nuclear speck / intracellular signal transduction / cadherin binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21-activated kinase 2, catalytic domain / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...p21-activated kinase 2, catalytic domain / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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
Similarity search - Domain/homology
D-MALATE / Serine/threonine-protein kinase PAK 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsHu, H.-F. / Luo, Z.P. / Wu, J.-W. / Wang, Z.-X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Ministry of Science and Technology (MoST, China) China
CitationJournal: Structure / Year: 2025
Title: Crystal structures of PAK2 reveal new insights into its autoinhibitory mechanism.
Authors: Hu, H.F. / Luo, Z. / Zhang, Y. / Fang, X. / Zhu, Z. / Wu, J.W. / Wang, Z.X.
History
DepositionJan 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 2
B: Serine/threonine-protein kinase PAK 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6804
Polymers103,4502
Non-polymers2302
Water19811
1
A: Serine/threonine-protein kinase PAK 2

A: Serine/threonine-protein kinase PAK 2


Theoretical massNumber of molelcules
Total (without water)103,4502
Polymers103,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area1880 Å2
ΔGint-14 kcal/mol
Surface area33730 Å2
MethodPISA
2
B: Serine/threonine-protein kinase PAK 2
hetero molecules

B: Serine/threonine-protein kinase PAK 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9116
Polymers103,4502
Non-polymers4604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.935, 166.935, 208.988
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-602-

SO4

21B-602-

SO4

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Components

#1: Protein Serine/threonine-protein kinase PAK 2 / Gamma-PAK / PAK65 / S6/H4 kinase / p21-activated kinase 2 / PAK-2 / p58


Mass: 51725.125 Da / Num. of mol.: 2 / Mutation: K278R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13177, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M DL-malic acid pH5.50, 1.3M (NH4)2SO4,3% methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 24956 / % possible obs: 99.8 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.2
Reflection shellResolution: 2.89→3 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.356 / Mean I/σ(I) obs: 2 / Num. unique obs: 4777 / CC1/2: 0.789 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→49.137 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.78 / SU ML: 0.311 / Cross valid method: FREE R-VALUE / ESU R: 0.948 / ESU R Free: 0.329
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2327 1251 5.013 %
Rwork0.1948 23705 -
all0.197 --
obs-24956 98.636 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 102.698 Å2
Baniso -1Baniso -2Baniso -3
1--3.705 Å2-1.852 Å20 Å2
2---3.705 Å20 Å2
3---12.018 Å2
Refinement stepCycle: LAST / Resolution: 2.89→49.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5402 0 14 11 5427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125507
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165435
X-RAY DIFFRACTIONr_angle_refined_deg1.691.6537447
X-RAY DIFFRACTIONr_angle_other_deg0.5261.56912573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.03522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.337101036
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.25210230
X-RAY DIFFRACTIONr_chiral_restr0.0810.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021123
X-RAY DIFFRACTIONr_nbd_refined0.2040.21013
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24562
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22702
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0860.266
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.229
X-RAY DIFFRACTIONr_nbd_other0.260.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3910.24
X-RAY DIFFRACTIONr_mcbond_it14.5069.9032742
X-RAY DIFFRACTIONr_mcbond_other14.4979.9032742
X-RAY DIFFRACTIONr_mcangle_it19.86517.8453417
X-RAY DIFFRACTIONr_mcangle_other19.86317.8463418
X-RAY DIFFRACTIONr_scbond_it15.40410.692765
X-RAY DIFFRACTIONr_scbond_other15.38910.6882760
X-RAY DIFFRACTIONr_scangle_it21.48619.3524030
X-RAY DIFFRACTIONr_scangle_other21.48119.3524025
X-RAY DIFFRACTIONr_lrange_it25.686117.20821697
X-RAY DIFFRACTIONr_lrange_other25.686117.20821698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.9640.366570.3891461X-RAY DIFFRACTION81.877
2.964-3.0450.354800.3181715X-RAY DIFFRACTION100
3.045-3.1330.308690.3061688X-RAY DIFFRACTION100
3.133-3.2290.299940.2571607X-RAY DIFFRACTION100
3.229-3.3350.291900.2441534X-RAY DIFFRACTION100
3.335-3.4510.218800.2191518X-RAY DIFFRACTION100
3.451-3.5810.266750.2081470X-RAY DIFFRACTION100
3.581-3.7260.232730.1791428X-RAY DIFFRACTION100
3.726-3.8910.19670.1761352X-RAY DIFFRACTION100
3.891-4.0790.27660.1631303X-RAY DIFFRACTION100
4.079-4.2980.21690.1541228X-RAY DIFFRACTION100
4.298-4.5570.18440.1411211X-RAY DIFFRACTION100
4.557-4.8690.185690.1431084X-RAY DIFFRACTION100
4.869-5.2540.236570.1581038X-RAY DIFFRACTION100
5.254-5.7490.29610.216934X-RAY DIFFRACTION100
5.749-6.4170.246370.2881X-RAY DIFFRACTION100
6.417-7.3890.22400.189779X-RAY DIFFRACTION100
7.389-8.9980.169580.17634X-RAY DIFFRACTION99.8557
8.998-12.5180.218380.185519X-RAY DIFFRACTION100
12.518-49.1370.313270.302321X-RAY DIFFRACTION100

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