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- PDB-3fy0: Crystal structure of PAK1 kinase domain with ruthenium complex DW1 -

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Basic information

Entry
Database: PDB / ID: 3fy0
TitleCrystal structure of PAK1 kinase domain with ruthenium complex DW1
ComponentsSerine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE / kinase / ATP-binding / phosphorylation / Allosteric enzyme / Apoptosis / Cell junction / Nucleotide-binding / Phosphoprotein / 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 / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / positive regulation of vascular associated smooth muscle cell migration / Activation of RAC1 / Ephrin signaling ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / positive regulation of vascular associated smooth muscle cell migration / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of fibroblast migration / regulation of axonogenesis / RHOV GTPase cycle / positive regulation of intracellular estrogen receptor signaling pathway / branching morphogenesis of an epithelial tube / establishment of cell polarity / RHOJ GTPase cycle / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / exocytosis / Fc-gamma receptor signaling pathway involved in phagocytosis / RHO GTPases activate PAKs / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / intercalated disc / Sema3A PAK dependent Axon repulsion / Smooth Muscle Contraction / positive regulation of protein targeting to membrane / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / positive regulation of axon extension / positive regulation of vascular associated smooth muscle cell proliferation / RHO GTPases activate PKNs / collagen binding / positive regulation of stress fiber assembly / neuron projection morphogenesis / ruffle / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / CD209 (DC-SIGN) signaling / cellular response to starvation / cerebellum development / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament / MAPK6/MAPK4 signaling / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / wound healing / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / cellular response to insulin stimulus / G beta:gamma signalling through CDC42 / cell migration / cell-cell junction / lamellipodium / chromosome / actin cytoskeleton organization / nuclear membrane / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / chromatin remodeling / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / dendrite / centrosome / DNA damage response / protein kinase binding / 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 / 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
Ruthenium pyridocarbazole / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 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 1.4Nov 6, 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)33,8642
Polymers33,3671
Non-polymers4961
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.050, 102.660, 122.341
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-DW1 / Ruthenium pyridocarbazole


Mass: 496.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H13N3O4Ru
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1M NaCl, 25% PEG 10000, 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: Nov 1, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 14267 / Num. obs: 14162 / % possible obs: 99.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 11.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 4 / % possible all: 100

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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: 2.35→47.14 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.541 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 716 5.1 %RANDOM
Rwork0.20161 ---
obs0.20451 13418 98.48 %-
all-13625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.699 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 31 119 2413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222342
X-RAY DIFFRACTIONr_angle_refined_deg1.3212.0163211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.72325.57995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56515414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.381510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021724
X-RAY DIFFRACTIONr_nbd_refined0.2010.21110
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.25
X-RAY DIFFRACTIONr_mcbond_it1.53121502
X-RAY DIFFRACTIONr_mcangle_it2.37532357
X-RAY DIFFRACTIONr_scbond_it1.52121093
X-RAY DIFFRACTIONr_scangle_it2.4073830
LS refinement shellResolution: 2.35→2.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 56 -
Rwork0.208 908 -
obs--90.09 %
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)
13.5626-2.6714-0.04065.01910.71341.08910.18340.2401-0.3145-0.4173-0.20620.4125-0.22690.00750.02280.02680.0357-0.0271-0.1253-0.0298-0.009521.53611.12151.766
21.02230.25430.01960.8844-0.00871.27310.04250.10680.0261-0.0772-0.0061-0.06190.0540.1263-0.0364-0.02520.02160.0273-0.0733-0.0101-0.012712.73435.13945.612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A249 - 344
2X-RAY DIFFRACTION2A345 - 541

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