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- PDB-9nbx: Crystal structure of PAK1 bound to C2 -

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Basic information

Entry
Database: PDB / ID: 9nbx
TitleCrystal structure of PAK1 bound to C2
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE / Kinase / inhibitor
Function / homology
Function and homology information


negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / regulation of axonogenesis ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / regulation of axonogenesis / phosphorylation / RHOV GTPase cycle / branching morphogenesis of an epithelial tube / positive regulation of intracellular estrogen receptor signaling pathway / RHOJ GTPase cycle / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / Fc-gamma receptor signaling pathway involved in phagocytosis / glutathione transferase / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / glutathione transferase activity / positive regulation of JUN kinase activity / Sema3A PAK dependent Axon repulsion / intercalated disc / ephrin receptor signaling pathway / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases activate PKNs / positive regulation of peptidyl-serine phosphorylation / collagen binding / positive regulation of stress fiber assembly / ruffle / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / CD209 (DC-SIGN) signaling / glutathione metabolic process / neuron projection morphogenesis / cellular response to starvation / Signal transduction by L1 / VEGFR2 mediated vascular permeability / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / wound healing / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / Z disc / ruffle membrane / G beta:gamma signalling through CDC42 / cell-cell junction / cell migration / lamellipodium / positive regulation of protein phosphorylation / chromosome / actin cytoskeleton organization / protein autophosphorylation / nuclear membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / chromatin remodeling / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / centrosome / dendrite / DNA damage response
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily / 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
: / Glutathione S-transferase class-mu 26 kDa isozyme / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, W. / Oh, A. / Kiefer, J.R. / Hsu, P.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Chem.Inf.Model. / Year: 2025
Title: Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions.
Authors: Walters, B.T. / Patapoff, A.W. / Kiefer, J.R. / Wu, P. / Wang, W.
History
DepositionFeb 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1
B: Glutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5385
Polymers122,6692
Non-polymers8693
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.818, 81.359, 65.854
Angle α, β, γ (deg.)90.00, 106.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1 / GST 26 / Sj26 antigen / SjGST / Alpha-PAK / p21-activated kinase 1 / PAK-1 / p65-PAK


Mass: 61334.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: Q13153, glutathione transferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1BW5 / (6M)-8-(3-aminopropyl)-6-(4-butoxy-2-methylphenyl)-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one


Mass: 395.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium Sulfate, 0.1M Tris pH8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 33900 / % possible obs: 97.8 % / Redundancy: 3.1 % / CC1/2: 0.996 / Rrim(I) all: 0.048 / Χ2: 1.006 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.15-2.192.60.50816690.570.8520.3590.6250.9397.6
2.19-2.232.70.48816980.60.8660.3390.5961.01298.4
2.23-2.272.80.42916890.710.9110.2920.5211.05698.7
2.27-2.322.80.38717200.7640.9310.2660.4721.06198.5
2.32-2.372.90.30616720.870.9650.2080.372198.6
2.37-2.4230.2817050.9080.9760.1870.3381.06498.7
2.42-2.4830.23917190.9220.980.1580.2881.08999
2.48-2.5530.20617160.9310.9820.1370.2481.13199.2
2.55-2.6230.17317040.9620.990.1140.2081.17398.7
2.62-2.713.10.14517210.9710.9930.0940.1741.11399.5
2.71-2.813.20.12117100.9810.9950.0780.1451.14599.7
2.81-2.923.20.10817320.9830.9960.0690.1291.16299.3
2.92-3.053.30.09617190.9860.9970.0610.1151.02399.6
3.05-3.213.30.08117300.9920.9980.0510.0960.95799.7
3.21-3.413.40.0717260.9910.9980.0440.0830.89599.8
3.41-3.683.30.06217360.9920.9980.0390.0730.79499.3
3.68-4.053.30.06916850.990.9980.0440.0820.94297.4
4.05-4.633.20.06916240.9860.9970.0460.0831.0893.4
4.63-5.833.20.05816710.9890.9970.0380.0690.92794.9
5.83-503.20.0415540.9960.9990.0260.0480.60586.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→31.93 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 1662 4.99 %
Rwork0.2246 --
obs0.2267 33297 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→31.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 62 41 4342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064369
X-RAY DIFFRACTIONf_angle_d0.7175922
X-RAY DIFFRACTIONf_dihedral_angle_d13.526601
X-RAY DIFFRACTIONf_chiral_restr0.049692
X-RAY DIFFRACTIONf_plane_restr0.01751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.3821480.32862614X-RAY DIFFRACTION98
2.21-2.280.31131210.29692685X-RAY DIFFRACTION99
2.28-2.370.28631300.26712631X-RAY DIFFRACTION99
2.37-2.460.2721490.25592650X-RAY DIFFRACTION99
2.46-2.570.31361410.25052653X-RAY DIFFRACTION99
2.57-2.710.27941340.24962678X-RAY DIFFRACTION99
2.71-2.880.31991420.24982647X-RAY DIFFRACTION100
2.88-3.10.31171570.23952685X-RAY DIFFRACTION100
3.1-3.410.29941350.23832687X-RAY DIFFRACTION100
3.41-3.90.23541430.20042670X-RAY DIFFRACTION99
3.91-4.920.22541370.19262529X-RAY DIFFRACTION94
4.92-31.930.24581250.2132506X-RAY DIFFRACTION90
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)
10.8587-0.2940.23870.4220.20560.7269-0.28620.3972-0.6494-0.26570.10010.2660.6086-0.521600.9081-0.00670.13290.8628-0.09020.927483.9991-23.47797.9763
23.77340.4603-2.10182.4584-0.00835.5079-0.0583-0.20870.0552-0.0106-0.0634-0.0746-0.44280.812-0.00030.4058-0.0285-0.06630.4941-0.01130.363985.7386-1.26421.4141
30.56960.7720.48091.07960.42721.2371-0.0316-0.16710.1520.42140.08410.21130.3944-0.31690.00010.6665-0.02980.03970.6603-0.07940.777859.2098-16.7098-16.0152
41.27320.61390.38822.2557-0.48392.2313-0.17240.156-0.11750.18740.05750.09540.2179-0.205400.4135-0.00540.02590.4222-0.05370.506871.4391-3.6015-20.3852
50.71260.11290.09090.4282-0.39771.22410.0129-0.5005-0.1140.42170.01810.1322-0.0574-0.11130.00020.56080.02940.03080.5491-0.05540.507374.63383.6649-8.9479
60.17770.0490.23810.04370.10750.32980.0768-0.0827-0.02490.45190.0363-0.3850.31250.84710.00010.69380.0396-0.00590.8066-0.09830.674687.93938.4432-10.1794
72.58911.1542-0.66840.8398-0.17551.8318-0.02690.14720.5070.15250.13870.2074-0.348-0.0723-0.00020.42230.0388-0.05070.4118-0.00910.538977.0397.5353-24.2468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 249 through 345 )
2X-RAY DIFFRACTION2chain 'A' and (resid 346 through 541 )
3X-RAY DIFFRACTION3chain 'B' and (resid 254 through 336 )
4X-RAY DIFFRACTION4chain 'B' and (resid 337 through 402 )
5X-RAY DIFFRACTION5chain 'B' and (resid 403 through 459 )
6X-RAY DIFFRACTION6chain 'B' and (resid 460 through 491 )
7X-RAY DIFFRACTION7chain 'B' and (resid 492 through 542 )

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