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- PDB-3fxz: Crystal structure of PAK1 kinase domain with ruthenium complex la... -

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Basic information

Entry
Database: PDB / ID: 3fxz
TitleCrystal structure of PAK1 kinase domain with ruthenium complex lambda-FL172
ComponentsSerine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE / Kinase / ATP-binding / Phosphorylation / Allosteric enzyme / Alternative splicing / Apoptosis / Cell junction / Cytoplasm / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase
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 / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / 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 / 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 / protein-containing complex / nucleoplasm / ATP binding
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 / 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
OCTAHEDRAL RU-PYRIDOCARBAZOLE / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMaksimoska, J. / Marmorstein, R. / Meggers, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Targeting Large Kinase Active Site with Rigid, Bulky Octahedral Ruthenium Complexes
Authors: Maksimoska, J. / Feng, L. / Harms, K. / Yi, C. / Kissil, J. / Marmorstein, R. / Meggers, E.
History
DepositionJan 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0352
Polymers33,3671
Non-polymers6681
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.183, 103.475, 122.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Serine/threonine-protein kinase PAK 1 / p21-activated kinase 1 / PAK-1 / p65-PAK / Alpha-PAK


Mass: 33367.242 Da / Num. of mol.: 1 / Fragment: UNP residues 249-545 / Mutation: K299R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13153, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-FLL / OCTAHEDRAL RU-PYRIDOCARBAZOLE


Mass: 668.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H18ClFN5O4Ru
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8.0, 1M NaCl, 25% PEG 4000, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.64→30 Å / Num. all: 40678 / Num. obs: 40150 / % possible obs: 98.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.5
Reflection shellResolution: 1.64→1.71 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3 / % possible all: 94.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→26.38 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.324 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21841 2019 5 %RANDOM
Rwork0.19499 ---
obs0.19618 38092 98.19 %-
all-38794 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.062 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.64→26.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 42 230 2539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222361
X-RAY DIFFRACTIONr_angle_refined_deg1.3242.0153231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89924.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5215413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5421512
X-RAY DIFFRACTIONr_chiral_restr0.090.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021745
X-RAY DIFFRACTIONr_nbd_refined0.2020.21118
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.218
X-RAY DIFFRACTIONr_mcbond_it2.06121522
X-RAY DIFFRACTIONr_mcangle_it2.78232389
X-RAY DIFFRACTIONr_scbond_it2.44121119
X-RAY DIFFRACTIONr_scangle_it3.5153833
X-RAY DIFFRACTIONr_sphericity_bonded11.79331
LS refinement shellResolution: 1.64→1.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 143 -
Rwork0.267 2441 -
obs--87.27 %

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