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- PDB-2qi8: Crystal structure of drug resistant SRC kinase domain -

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Basic information

Entry
Database: PDB / ID: 2qi8
TitleCrystal structure of drug resistant SRC kinase domain
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsSIGNALING PROTEIN / TRANSFERASE / Src kinase domain / drug resistance
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Recycling pathway of L1 / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / regulation of cell cycle / cell adhesion / cell cycle / phosphorylation / signaling receptor binding / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / 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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsMichalczyk, A. / Rode, H.B. / Gruetter, C. / Rauh, D.
CitationJournal: Bioorg.Med.Chem. / Year: 2008
Title: Structural insights into how irreversible inhibitors can overcome drug resistance in EGFR.
Authors: Michalczyk, A. / Kluter, S. / Rode, H.B. / Simard, J.R. / Grutter, C. / Rabiller, M. / Rauh, D.
History
DepositionJul 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6383
Polymers65,5462
Non-polymers921
Water3,099172
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8652
Polymers32,7731
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)32,7731
Polymers32,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.000, 63.020, 73.950
Angle α, β, γ (deg.)78.780, 88.800, 90.140
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / / E.C.2.7.10.2 / p60-Src / c-Src / pp60c-src


Mass: 32772.801 Da / Num. of mol.: 2 / Mutation: T338M, S345C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pSKB3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19% Ethylene glycol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2006 / Details: Osmic
RadiationMonochromator: Multilayer Optic (Rigaku) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.32→72.548 Å / Num. all: 32189 / Num. obs: 30194 / % possible obs: 93.8 % / Redundancy: 2.2 % / Biso Wilson estimate: 38.452 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.32-2.450.372.1930243260.3791.6
2.45-2.590.2912.6891440890.29192.4
2.59-2.770.2381.3849938960.23893
2.77-30.1415.4801736630.14193.5
3-3.280.0918.4735233580.09194.2
3.28-3.670.0619.6665430420.06194.7
3.67-4.240.04412.8601227540.04495.4
4.24-5.190.03220.7499622890.03295.7
5.19-7.340.03620.1390417880.03696.5
7.34-43.070.02719.321469890.02796.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→72.548 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.867 / SU B: 7.196 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1546 5.1 %RANDOM
Rwork0.205 ---
all0.209 32189 --
obs0.209 30188 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20.02 Å2-0.4 Å2
2---0.48 Å20.76 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.32→72.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 6 172 4169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224141
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9765619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7975510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35223.838185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04515714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3921528
X-RAY DIFFRACTIONr_chiral_restr0.1170.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023128
X-RAY DIFFRACTIONr_nbd_refined0.2220.22068
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.27
X-RAY DIFFRACTIONr_mcbond_it0.891.52618
X-RAY DIFFRACTIONr_mcangle_it1.52424069
X-RAY DIFFRACTIONr_scbond_it2.13931792
X-RAY DIFFRACTIONr_scangle_it3.2154.51543
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 121 -
Rwork0.247 2056 -
obs-2177 91.7 %

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