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- PDB-2hy8: PAK1 complex with ST2001 -

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Basic information

Entry
Database: PDB / ID: 2hy8
TitlePAK1 complex with ST2001
ComponentsSerine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE / Typical fold of Ser/Thr kinases. Inhibitor is bound between the N-terminal and C-terminal domains.
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 / DSCAM interactions / RHOV GTPase cycle / regulation of axonogenesis / branching morphogenesis of an epithelial tube / Fc-gamma receptor signaling pathway involved in phagocytosis / RHOJ GTPase cycle / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / stimulatory C-type lectin receptor signaling pathway / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / Generation of second messenger molecules / intercalated disc / Smooth Muscle Contraction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / localization / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of JUN kinase activity / positive regulation of stress fiber assembly / ruffle / RAC1 GTPase cycle / EPHB-mediated forward signaling / collagen binding / CD209 (DC-SIGN) signaling / neuron projection morphogenesis / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / wound healing / G beta:gamma signalling through CDC42 / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / 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 / positive regulation of cell migration / intracellular signal transduction / chromatin remodeling / positive regulation of protein phosphorylation / axon / phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / apoptotic process / DNA damage response / positive regulation of cell population proliferation / 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 / 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-1ST / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchulze-Gahmen, U. / Lu, H.
CitationJournal: To be Published
Title: Crystal Structure of the Complex Between Human Pak1-kinase and 3-Hydroxystaurosporine
Authors: Lu, H. / Lei, M. / Schulze-Gahmen, U.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,7822
Polymers33,3011
Non-polymers4811
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.865, 103.828, 123.193
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: 33301.242 Da / Num. of mol.: 1 / Fragment: kinase domain (residues 249-545) / Mutation: K299R, T423E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13153, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1ST / (5S,6R,7R,9R)-12-HYDROXY-6-METHOXY-5-METHYL-7-(METHYLAMINO)-6,7,8,9-TETRAHYDRO-5H,14H-5,9-EPOXY-4B,9A,15-TRIAZADIBENZO[ B,H]CYCLONONA[1,2,3,4-JKL]CYCLOPENTA[E]-AS-INDACEN-14-ONE / 3-HYDROXYSTAUROSPORINE


Mass: 480.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24N4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 ration of protein and precipitant. Precipitant: 0.13 M PIPES pH 6.5, 1.5 M NaCl, 23% PEG 4000, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2005
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.68 Å / Num. all: 21719 / Num. obs: 21719 / Observed criterion σ(F): 0 / Biso Wilson estimate: 21.3 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 51 / Limit k min: 0 / Limit l max: 61 / Limit l min: 0 / Observed criterion F max: 212108.56 / Observed criterion F min: 0.32
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 2.7 / % possible all: 83.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.68 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: CNS Parameter files: CNS_TOPPAR/protein_rep.param CNS_TOPPAR/water_rep.param ../sto_xplor_par.txt CNS Topology files: CNS_TOPPAR/protein.top CNS_TOPPAR/water.top ../sto_xplor_top.txt
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1020 4.9 %Random
Rwork0.208 ---
all-22463 --
obs-20899 93 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 62.3936 Å2 / ksol: 0.349578 e/Å3
Displacement parametersBiso max: 77.51 Å2 / Biso mean: 36.4 Å2 / Biso min: 19.19 Å2
Baniso -1Baniso -2Baniso -3
1-12.77 Å20 Å20 Å2
2---8.43 Å20 Å2
3----4.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.17 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 36 192 2437
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.090.231014.80.25320200.0232753212177
2.09-2.20.2331214.90.22823560.0212786247788.9
2.2-2.340.23713150.21824740.0212763260594.3
2.34-2.520.2213550.20625400.0192802267595.5
2.52-2.770.2481144.30.22225610.0232778267596.3
2.77-3.170.2481545.60.23326020.022823275697.6
3.17-40.2221274.60.20326280.022819275597.7
4-45.680.2361374.80.18426980.022962283595.7

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