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- PDB-5y80: Complex structure of cyclin G-associated kinase with gefitinib -

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Basic information

Entry
Database: PDB / ID: 5y80
TitleComplex structure of cyclin G-associated kinase with gefitinib
Components
  • Cyclin-G-associated kinaseGAK (protein)
  • NANOBODYSingle-domain antibody
KeywordsTRANSFERASE/IMMUNE SYSTEM / kinase / complex / TRANSFERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of clathrin coat assembly / synaptic vesicle uncoating / Golgi to lysosome transport / protein localization to Golgi apparatus / clathrin coat assembly / clathrin coat disassembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding ...regulation of clathrin coat assembly / synaptic vesicle uncoating / Golgi to lysosome transport / protein localization to Golgi apparatus / clathrin coat assembly / clathrin coat disassembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding / Golgi Associated Vesicle Biogenesis / Golgi organization / chaperone cofactor-dependent protein refolding / intracellular transport / receptor-mediated endocytosis / cyclin binding / protein localization to plasma membrane / negative regulation of neuron projection development / presynapse / Clathrin-mediated endocytosis / protein-folding chaperone binding / vesicle / non-specific serine/threonine protein kinase / cell cycle / phosphorylation / focal adhesion / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain ...Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / C2 domain superfamily / Protein-tyrosine phosphatase-like / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gefitinib / Cyclin-G-associated kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOhbayashi, N. / Murayama, K. / Kato-Murayama, M. / Shirouzu, M.
CitationJournal: ChemistryOpen / Year: 2018
Title: Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib.
Authors: Ohbayashi, N. / Murayama, K. / Kato-Murayama, M. / Kukimoto-Niino, M. / Uejima, T. / Matsuda, T. / Ohsawa, N. / Yokoyoma, S. / Nojima, H. / Shirouzu, M.
History
DepositionAug 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-G-associated kinase
B: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7414
Polymers51,8472
Non-polymers8942
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-18 kcal/mol
Surface area20310 Å2
Unit cell
Length a, b, c (Å)70.331, 73.870, 95.311
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 Cyclin-G-associated kinase / GAK (protein)


Mass: 35657.766 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAK / Details (production host): Cell-Free protein synthesis / Production host: Escherichia coli (E. coli)
References: UniProt: O14976, non-specific serine/threonine protein kinase
#2: Antibody NANOBODY / Single-domain antibody


Mass: 16189.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Details (production host): Cell-Free protein synthesis / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-IRE / Gefitinib / Gefitinib


Mass: 446.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24ClFN4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate,0.1 M sodium cacodylate trihydrate (pH 6.5), 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.7 Å / Num. obs: 17801 / % possible obs: 100 % / Redundancy: 9.3 % / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 1968 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_743)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C57

4c57


Resolution: 2.5→44.924 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.49
RfactorNum. reflection% reflection
Rfree0.2819 951 5.36 %
Rwork0.2295 --
obs0.2324 17740 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 62 60 3524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053549
X-RAY DIFFRACTIONf_angle_d1.0944796
X-RAY DIFFRACTIONf_dihedral_angle_d20.231328
X-RAY DIFFRACTIONf_chiral_restr0.039514
X-RAY DIFFRACTIONf_plane_restr0.003615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.63190.35491320.25582372X-RAY DIFFRACTION100
2.6319-2.79680.36691290.26252344X-RAY DIFFRACTION100
2.7968-3.01260.3662960.26392402X-RAY DIFFRACTION100
3.0126-3.31570.32641380.27072380X-RAY DIFFRACTION100
3.3157-3.79530.34631450.26632375X-RAY DIFFRACTION100
3.7953-4.78080.20751430.19072407X-RAY DIFFRACTION100
4.7808-44.9310.22931680.19072509X-RAY DIFFRACTION100

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