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- PDB-3dkc: Structure of MET receptor tyrosine kinase in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 3dkc
TitleStructure of MET receptor tyrosine kinase in complex with ATP
ComponentsHepatocyte growth factor receptorC-Met
KeywordsONCOPROTEIN / DRUG DISCOVERY / c-MET KINASE / FRAGMENT BASED / Membrane / Receptor / Transmembrane
Function / homology
Function and homology information


hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity ...hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity / MET receptor recycling / Sema4D mediated inhibition of cell attachment and migration / MET activates PTPN11 / pancreas development / negative regulation of Rho protein signal transduction / MET activates PI3K/AKT signaling / MET activates RAP1 and RAC1 / negative regulation of stress fiber assembly / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / establishment of skin barrier / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / MET activates RAS signaling / phagocytosis / negative regulation of autophagy / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / Negative regulation of MET activity / neuron differentiation / receptor protein-tyrosine kinase / transmembrane receptor protein tyrosine kinase activity / positive regulation of kinase activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / transmembrane receptor protein tyrosine kinase signaling pathway / cell migration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of protein kinase B signaling / protein phosphatase binding / cell surface receptor signaling pathway / receptor complex / cell surface / signal transduction / plasma membrane => GO:0005886 / positive regulation of transcription by RNA polymerase II / extracellular region / membrane => GO:0016020 / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain superfamily / Sema domain profile. / Sema domain / IPT/TIG domain ...Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain superfamily / Sema domain profile. / Sema domain / IPT/TIG domain / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / Tyrosine kinase, catalytic domain / Tyrosine-protein 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 / WD40/YVTN repeat-like-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinases ATP-binding region signature. / Protein kinase, ATP binding site / Immunoglobulin-like fold / 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
ADENOSINE-5'-TRIPHOSPHATE / Hepatocyte growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.52 Å
AuthorsHendle, J.
CitationJournal: Mol.Cancer Ther. / Year: 2009
Title: SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo.
Authors: Buchanan, S.G. / Hendle, J. / Lee, P.S. / Smith, C.R. / Bounaud, P.Y. / Jessen, K.A. / Tang, C.M. / Huser, N.H. / Felce, J.D. / Froning, K.J. / Peterman, M.C. / Aubol, B.E. / Gessert, S.F. / ...Authors: Buchanan, S.G. / Hendle, J. / Lee, P.S. / Smith, C.R. / Bounaud, P.Y. / Jessen, K.A. / Tang, C.M. / Huser, N.H. / Felce, J.D. / Froning, K.J. / Peterman, M.C. / Aubol, B.E. / Gessert, S.F. / Sauder, J.M. / Schwinn, K.D. / Russell, M. / Rooney, I.A. / Adams, J. / Leon, B.C. / Do, T.H. / Blaney, J.M. / Sprengeler, P.A. / Thompson, D.A. / Smyth, L. / Pelletier, L.A. / Atwell, S. / Holme, K. / Wasserman, S.R. / Emtage, S. / Burley, S.K. / Reich, S.H.
History
DepositionJun 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Structure summary
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_conn_angle ...citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Hepatocyte growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3174
Polymers35,7501
Non-polymers5673
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.027, 45.083, 167.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hepatocyte growth factor receptor / C-Met / HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / ...HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / Tyrosine-protein kinase Met


Mass: 35750.348 Da / Num. of mol.: 1 / Mutation: Y1194F, Y1234F, Y1235D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET, hCG_38705, tcag7.66 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08581
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.2
Details: 11% ISOPROPANOL, 2.5% PEG 5K MME, 100 mM BIS-TRIS, pH 6.2, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97969 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 8, 2005
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionResolution: 1.52→21.115 Å / Num. obs: 50425 / % possible obs: 98.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.7

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.52→21.1 Å / Occupancy max: 1 / Occupancy min: 0.35 /
RfactorNum. reflection
Rfree0.218 -
Rwork0.189 -
obs-50425
Displacement parametersBiso max: 53.4 Å2 / Biso mean: 17.217 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 1.52→21.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 33 333 2817

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