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- PDB-5y7z: Complex structure of cyclin G-associated kinase with gefitinib -

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Basic information

Entry
Database: PDB / ID: 5y7z
TitleComplex structure of cyclin G-associated kinase with gefitinib
Components
  • Cyclin-G-associated kinase
  • NANOBODY
KeywordsTRANSFERASE/IMMUNE SYSTEM / Kinase / complex / TRANSFERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of clathrin coat assembly / Golgi to lysosome transport / synaptic vesicle uncoating / clathrin coat disassembly / protein localization to Golgi apparatus / clathrin coat assembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding ...regulation of clathrin coat assembly / Golgi to lysosome transport / synaptic vesicle uncoating / clathrin coat disassembly / protein localization to Golgi apparatus / clathrin coat assembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding / Golgi Associated Vesicle Biogenesis / Golgi organization / : / intracellular transport / receptor-mediated endocytosis / cyclin binding / protein localization to plasma membrane / presynapse / Clathrin-mediated endocytosis / negative regulation of neuron projection development / protein-folding chaperone binding / vesicle / non-specific serine/threonine protein kinase / protein serine kinase activity / focal adhesion / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / membrane / cytosol
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 / Protein-tyrosine phosphatase-like / C2 domain superfamily / 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: 2.804 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
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.pdbx_stereo_config / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,06911
Polymers103,6954
Non-polymers1,3747
Water1629
1
A: Cyclin-G-associated kinase
C: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5836
Polymers51,8472
Non-polymers7354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclin-G-associated kinase
D: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4875
Polymers51,8472
Non-polymers6393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.353, 85.513, 149.042
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


Mass: 35657.766 Da / Num. of mol.: 2 / 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


Mass: 16189.729 Da / Num. of mol.: 2
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


Mass: 446.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24ClFN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.17 M ammonium sulfate, 0.085 M sodium cacodylate trihydrate (pH 6.5), 25.5% PEG 8000, 15% glycerol

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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: Jul 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 23845 / % possible obs: 97 % / Redundancy: 3.3 % / Net I/σ(I): 5.3
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 1587 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C57

4c57


Resolution: 2.804→45.251 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.08
RfactorNum. reflection% reflection
Rfree0.288 1199 5.04 %
Rwork0.2327 --
obs0.2355 23789 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.804→45.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6898 0 87 9 6994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047126
X-RAY DIFFRACTIONf_angle_d1.0449630
X-RAY DIFFRACTIONf_dihedral_angle_d16.0432674
X-RAY DIFFRACTIONf_chiral_restr0.0361036
X-RAY DIFFRACTIONf_plane_restr0.0021244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8042-2.91640.41891490.32912402X-RAY DIFFRACTION95
2.9164-3.04910.33071340.3032499X-RAY DIFFRACTION98
3.0491-3.20980.31511320.28552489X-RAY DIFFRACTION98
3.2098-3.41090.31441300.25852531X-RAY DIFFRACTION98
3.4109-3.67410.28861410.23442491X-RAY DIFFRACTION97
3.6741-4.04370.27861270.20642512X-RAY DIFFRACTION97
4.0437-4.62830.21781220.19022538X-RAY DIFFRACTION97
4.6283-5.82920.23971350.20542529X-RAY DIFFRACTION96
5.8292-45.25720.30511290.2042599X-RAY DIFFRACTION94

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