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- PDB-2z8c: Phosphorylated insulin receptor tyrosine kinase in complex with (... -

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Basic information

Entry
Database: PDB / ID: 2z8c
TitlePhosphorylated insulin receptor tyrosine kinase in complex with (4-{[5-carbamoyl-4-(3-methylanilino)pyrimidin-2-yl]amino}phenyl)acetic acid
Components
  • 6-mer peptide from Insulin receptor substrate 1
  • Insulin receptor
KeywordsTRANSFERASE / Alternative splicing / ATP-binding / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Polymorphism / Receptor / Transmembrane / Tyrosine-protein kinase / Transducer
Function / homology
Function and homology information


IRS-related events triggered by IGF1R / regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex ...IRS-related events triggered by IGF1R / regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / positive regulation of glucose metabolic process / insulin-like growth factor I binding / insulin receptor activity / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by Leptin / positive regulation of protein-containing complex disassembly / cargo receptor activity / PI3K/AKT activation / dendritic spine maintenance / cellular response to fatty acid / insulin binding / PTB domain binding / adrenal gland development / Signaling by ALK / neuronal cell body membrane / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / amyloid-beta clearance / positive regulation of respiratory burst / positive regulation of receptor internalization / regulation of embryonic development / transport across blood-brain barrier / SOS-mediated signalling / insulin receptor substrate binding / PI3K Cascade / positive regulation of glycogen biosynthetic process / epidermis development / negative regulation of insulin secretion / Signal attenuation / phosphatidylinositol 3-kinase binding / heart morphogenesis / Growth hormone receptor signaling / positive regulation of insulin receptor signaling pathway / dendrite membrane / Insulin receptor recycling / neuron projection maintenance / negative regulation of insulin receptor signaling pathway / Interleukin-7 signaling / positive regulation of glycolytic process / activation of protein kinase B activity / phosphotyrosine residue binding / SH2 domain binding / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin-like growth factor receptor signaling pathway / receptor-mediated endocytosis / learning / caveola / positive regulation of glucose import / protein kinase C binding / insulin-like growth factor receptor binding / positive regulation of MAP kinase activity / insulin receptor binding / response to insulin / receptor internalization / receptor protein-tyrosine kinase / memory / cellular response to growth factor stimulus / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / positive regulation of nitric oxide biosynthetic process / Signaling by ALK fusions and activated point mutants / signaling receptor complex adaptor activity / late endosome / insulin receptor signaling pathway / PIP3 activates AKT signaling / glucose homeostasis / amyloid-beta binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / receptor complex / endosome membrane / positive regulation of cell migration / symbiont entry into host cell / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / protein domain specific binding / external side of plasma membrane / axon
Similarity search - Function
Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Phosphotyrosine-binding domain / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site ...Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Phosphotyrosine-binding domain / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / PH domain / Growth factor receptor cysteine-rich domain superfamily / PH domain profile. / Pleckstrin homology domain. / Fibronectin type III domain / Pleckstrin homology domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / 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. / 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
Chem-S91 / Insulin receptor / Insulin receptor substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsKatayama, N. / Kurihara, H.
CitationJournal: Proteins / Year: 2008
Title: Identification of a key element for hydrogen-bonding patterns between protein kinases and their inhibitors.
Authors: Katayama, N. / Orita, M. / Yamaguchi, T. / Hisamichi, H. / Kuromitsu, S. / Kurihara, H. / Sakashita, H. / Matsumoto, Y. / Fujita, S. / Niimi, T.
History
DepositionSep 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin receptor
B: 6-mer peptide from Insulin receptor substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8273
Polymers35,4492
Non-polymers3771
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-5 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.540, 71.540, 133.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Insulin receptor / IR / CD220 ANTIGEN


Mass: 34689.320 Da / Num. of mol.: 1 / Fragment: TYROSINE KINASE DOMAIN / Mutation: C981S, Y984F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell line (production host): SF9 / Cellular location (production host): CYTOPLASM / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P06213, receptor protein-tyrosine kinase
#2: Protein/peptide 6-mer peptide from Insulin receptor substrate 1 / IRS-1


Mass: 759.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRS1 / Cell line (production host): SF9 / Cellular location (production host): CYTOPLASM / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P35568
#3: Chemical ChemComp-S91 / [4-({5-(AMINOCARBONYL)-4-[(3-METHYLPHENYL)AMINO]PYRIMIDIN-2-YL}AMINO)PHENYL]ACETIC ACID / (4-{[5-CARBAMOYL-4-(3-METHYLANILINO)PYRIMIDIN-2-YL]AMINO}PHENYL)ACETIC ACID


Mass: 377.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N5O3

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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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growMethod: vapor diffusion, hanging drop / Details: PEG 3350, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jan 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→56.23 Å / Num. obs: 6395 / % possible obs: 98.7 % / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
CNX2002refinement
MOSFLMdata reduction
SCALAdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IR3

1ir3


Resolution: 3.25→56.23 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1313049.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 683 10.7 %RANDOM
Rwork0.217 ---
obs-6349 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.78 Å2 / ksol: 0.24 e/Å3
Displacement parametersBiso mean: 60.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.18 Å213.16 Å20 Å2
2---4.18 Å20 Å2
3---8.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 3.25→56.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 28 0 2466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.622
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 3.25→3.45 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 106 10.1 %
Rwork0.248 939 -
obs--96.9 %

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