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- PDB-1u46: Crystal Structure of the Unphosphorylated Kinase Domain of the Ty... -

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Basic information

Entry
Database: PDB / ID: 1u46
TitleCrystal Structure of the Unphosphorylated Kinase Domain of the Tyrosine Kinase ACK1
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE / Tyrosine Kinase
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLougheed, J.C. / Chen, R.H. / Mak, P. / Stout, T.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the Cdc42-associated Tyrosine Kinase ACK1.
Authors: Lougheed, J.C. / Chen, R.H. / Mak, P. / Stout, T.J.
History
DepositionJul 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Activated CDC42 kinase 1
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1523
Polymers66,1162
Non-polymers351
Water4,143230
1
A: Activated CDC42 kinase 1


Theoretical massNumber of molelcules
Total (without water)33,0581
Polymers33,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0942
Polymers33,0581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.176, 43.401, 84.452
Angle α, β, γ (deg.)90.00, 111.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Activated CDC42 kinase 1 / ACK-1


Mass: 33058.047 Da / Num. of mol.: 2 / Fragment: Kinase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACK1 / Cell line (production host): Sf-9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q07912, EC: 2.7.1.112
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.1 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, magnesium chloride, sodium chloride, HEPES, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 37422 / Num. obs: 37411 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.4 Å2 / Rsym value: 0.078 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.11 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.473 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 1886 5 %RANDOM
Rwork0.19944 ---
all0.202 37401 --
obs0.20201 35515 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.916 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-1.07 Å2
2--2.19 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 1 230 4340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214201
X-RAY DIFFRACTIONr_bond_other_d0.0020.023901
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.965675
X-RAY DIFFRACTIONr_angle_other_deg0.91539043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145503
X-RAY DIFFRACTIONr_chiral_restr0.1070.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024576
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02871
X-RAY DIFFRACTIONr_nbd_refined0.210.2821
X-RAY DIFFRACTIONr_nbd_other0.240.24437
X-RAY DIFFRACTIONr_nbtor_other0.0870.22483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.211
X-RAY DIFFRACTIONr_mcbond_it1.0881.52543
X-RAY DIFFRACTIONr_mcangle_it1.93224089
X-RAY DIFFRACTIONr_scbond_it2.65931658
X-RAY DIFFRACTIONr_scangle_it4.2044.51586
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 147
Rwork0.248 2626

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