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- PDB-4ks8: PAK6 kinase domain in complex with sunitinib -

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Basic information

Entry
Database: PDB / ID: 4ks8
TitlePAK6 kinase domain in complex with sunitinib
ComponentsSerine/threonine-protein kinase PAK 6
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase / Phosphotransfer / Phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


neuron projection arborization / RHOD GTPase cycle / Activation of RAC1 / neuron projection extension / RHOV GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / cytoskeleton organization / RAC1 GTPase cycle ...neuron projection arborization / RHOD GTPase cycle / Activation of RAC1 / neuron projection extension / RHOV GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / cytoskeleton organization / RAC1 GTPase cycle / locomotory behavior / learning / memory / fibrillar center / cell junction / postsynaptic density / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of DNA-templated transcription / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase PAK 6 / 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 ...Serine/threonine-protein kinase PAK 6 / 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 / Protein kinase 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-B49 / Serine/threonine-protein kinase PAK 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGao, J. / Boggon, T.J.
CitationJournal: Plos One / Year: 2013
Title: Substrate and Inhibitor Specificity of the Type II p21-Activated Kinase, PAK6.
Authors: Gao, J. / Ha, B.H. / Lou, H.J. / Morse, E.M. / Zhang, R. / Calderwood, D.A. / Turk, B.E. / Boggon, T.J.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Dec 4, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7002
Polymers33,3021
Non-polymers3981
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.616, 60.099, 99.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase PAK 6 / PAK-5 / p21-activated kinase 6 / PAK-6


Mass: 33301.551 Da / Num. of mol.: 1 / Fragment: Kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK6, PAK5 / Plasmid: pET-32 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NQU5, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-B49 / N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide / SUNITINIB / Sunitinib


Mass: 398.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27FN4O2 / Comment: medication, anticancer, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% (v/v) isopropanol, 0.1M MES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 18, 2012 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 22562 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.117 / Net I/σ(I): 17.47
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 2187 / Rsym value: 0.885 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KS7

4ks7


Resolution: 1.95→38.46 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.357 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26099 1149 5.1 %RANDOM
Rwork0.21813 ---
obs0.22026 21308 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.004 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--1.04 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 29 171 2493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192372
X-RAY DIFFRACTIONr_bond_other_d0.0010.022340
X-RAY DIFFRACTIONr_angle_refined_deg1.33723215
X-RAY DIFFRACTIONr_angle_other_deg0.70835382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50223.75104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23515432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4711519
X-RAY DIFFRACTIONr_chiral_restr0.0670.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02520
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 72 -
Rwork0.304 1502 -
obs--95.68 %

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