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- PDB-4daw: Crystal structure of PAK1 kinase domain with the ruthenium phthal... -

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Basic information

Entry
Database: PDB / ID: 4daw
TitleCrystal structure of PAK1 kinase domain with the ruthenium phthalimide complex
ComponentsSerine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Serine/threonine kinase / phosphorylation / ATP-binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway ...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 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / RHOV GTPase cycle / branching morphogenesis of an epithelial tube / regulation of axonogenesis / RHOJ GTPase cycle / stimulatory C-type lectin receptor signaling pathway / regulation of MAPK cascade / RHOQ GTPase cycle / RHO GTPases activate PAKs / exocytosis / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / intercalated disc / ephrin receptor signaling pathway / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / phosphorylation / RHO GTPases activate PKNs / positive regulation of JUN kinase activity / positive regulation of stress fiber assembly / ruffle / collagen binding / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / CD209 (DC-SIGN) signaling / neuron projection morphogenesis / VEGFR2 mediated vascular permeability / Signal transduction by L1 / regulation of actin cytoskeleton organization / actin filament / FCERI mediated MAPK activation / wound healing / MAPK6/MAPK4 signaling / Z disc / Regulation of actin dynamics for phagocytic cup formation / G beta:gamma signalling through CDC42 / ruffle membrane / cell-cell junction / cell migration / lamellipodium / positive regulation of peptidyl-serine phosphorylation / chromosome / actin cytoskeleton organization / nuclear membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / chromatin remodeling / positive regulation of protein phosphorylation / protein phosphorylation / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / centrosome / DNA damage response / positive regulation of cell population proliferation / dendrite / apoptotic process / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / : / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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
Chem-0H2 / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaksimoska, J. / Marmorstein, R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: The art of filling protein pockets efficiently with octahedral metal complexes.
Authors: Blanck, S. / Maksimoska, J. / Baumeister, J. / Harms, K. / Marmorstein, R. / Meggers, E.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.3Oct 16, 2024Group: Structure summary / Category: 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)33,9302
Polymers33,3671
Non-polymers5631
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.676, 103.549, 122.790
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 / Alpha-PAK / p21-activated kinase 1 / PAK-1 / p65-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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13153, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-0H2 / [1,3-dioxo-6-(pyridin-2-yl-kappaN)-2,3-dihydro-1H-isoindol-5-yl-kappaC~5~][(thioxomethylidene)azanido-kappaN](1,4,7-trithionane-kappa~3~S~1~,S~4~,S~7~)ruthenium


Mass: 562.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O2RuS4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25 PEG 4000, 1 M NaCl, 10 mM DTT, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 12, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 22816 / Num. obs: 22771 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.137 / Rsym value: 0.098 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2210 / Rsym value: 0.561 / % possible all: 98.5

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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
Starting model: PDB ENTRY 3FXZ

3fxz


Resolution: 2→27.95 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.735 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23761 1163 5.1 %RANDOM
Rwork0.20109 ---
obs0.20296 21570 99.94 %-
all-21582 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.495 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 30 205 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222390
X-RAY DIFFRACTIONr_angle_refined_deg1.3732.0033263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4015311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58525.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37315426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8751511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021752
X-RAY DIFFRACTIONr_nbd_refined0.1920.21126
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2181
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.222
X-RAY DIFFRACTIONr_mcbond_it0.6021.51538
X-RAY DIFFRACTIONr_mcangle_it1.02622420
X-RAY DIFFRACTIONr_scbond_it1.38931040
X-RAY DIFFRACTIONr_scangle_it2.2824.5831
LS refinement shellResolution: 1.998→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 90 -
Rwork0.221 1535 -
obs--99.33 %

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