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- PDB-8fe9: Crystal structure of Ack1 kinase K161Q mutant in complex with the... -

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Basic information

Entry
Database: PDB / ID: 8fe9
TitleCrystal structure of Ack1 kinase K161Q mutant in complex with the selective inhibitor (R)-9b
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / tyrosine kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity ...regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / adherens junction / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytoplasmic vesicle membrane / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / Cdc42 binding domain-like / Mig-6 domain / GTPase binding / EGFR receptor inhibitor Mig-6 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / Cdc42 binding domain-like / Mig-6 domain / GTPase binding / EGFR receptor inhibitor Mig-6 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
Similarity search - Domain/homology
Chem-R9B / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPaung, Y. / Kan, Y. / Seeliger, M.S. / Miller, W.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119437 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI164424 United States
Department of Veterans Affairs (VA, United States)BX002292 United States
CitationJournal: Biochemistry / Year: 2023
Title: Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk.
Authors: Kan, Y. / Paung, Y. / Kim, Y. / Seeliger, M.A. / Miller, W.T.
History
DepositionDec 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9802
Polymers32,4371
Non-polymers5431
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.690, 91.690, 190.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Activated CDC42 kinase 1 / ACK-1 / Tyrosine kinase non-receptor protein 2


Mass: 32437.344 Da / Num. of mol.: 1 / Mutation: K161Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNK2, ACK1 / Plasmid: pFASTBAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary
References: UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-R9B / N-[(1S)-1-benzyl-2-[(6-chloro-2-oxo-1H-quinolin-4-yl)methylamino]-2-oxo-ethyl]-4-hydroxy-2-oxo-1H-quinoline-6-carbo


Mass: 542.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H23ClN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05 M Bis-Tris (pH 5.8), 19% PEG3350, 0.3 M MgCl2, 2.5% glycerol
PH range: 6.0-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→28.99 Å / Num. obs: 7020 / % possible obs: 99 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 19.6
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 1.088 / Num. unique obs: 624 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→28.99 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2534 697 10.01 %
Rwork0.2005 6267 -
obs0.206 6964 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 39 5 2249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192302
X-RAY DIFFRACTIONf_angle_d0.56273121
X-RAY DIFFRACTIONf_chiral_restr0.0408334
X-RAY DIFFRACTIONf_plane_restr0.0037401
X-RAY DIFFRACTIONf_dihedral_angle_d15.1745853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.37661320.26751175X-RAY DIFFRACTION95.96
3.45-3.790.27641360.21741229X-RAY DIFFRACTION99.64
3.79-4.340.2491390.19041250X-RAY DIFFRACTION99.64
4.34-5.460.22731410.19051265X-RAY DIFFRACTION99.86
5.47-28.990.24021490.19341348X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 33.8745121239 Å / Origin y: 18.4514654772 Å / Origin z: 24.6697009095 Å
111213212223313233
T0.611265432606 Å2-0.0583147766605 Å20.0476000770063 Å2-0.486377532458 Å2-0.100097196433 Å2--0.592900515021 Å2
L3.42566109243 °20.133981223024 °2-2.05969507769 °2-5.39774522189 °2-3.722033244 °2--8.60658090117 °2
S-0.053008130425 Å °0.0855584360318 Å °-0.524732719133 Å °-0.186946464021 Å °-0.0481671817689 Å °0.117002225181 Å °0.970830587665 Å °0.071463518021 Å °0.0569521552533 Å °
Refinement TLS groupSelection details: all

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