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- PDB-3qlf: Crystal structure of the L317I mutant of the C-src tyrosine kinas... -

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Basic information

Entry
Database: PDB / ID: 3qlf
TitleCrystal structure of the L317I mutant of the C-src tyrosine kinase domain complexed with pyrazolopyrimidine 5
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / C-SRC L317I MUTANT / TYROSINE KINASE / PYRAZOLOPYRIMIDINE 5
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 / Src homology 3 domains / SH2 domain / 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 / Src homology 3 domains / SH2 domain / 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
Chem-PD5 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBoubeva, R. / Pernot, L. / Perozzo, R. / Scapozza, L.
Citation
Journal: To be Published
Title: A single amino-acid dictates the dynamics of the switch between active and inactive C-src conformation
Authors: Boubeva, R. / Pernot, L. / Cristiani, A. / Moretti, L. / Berteotti, A. / Perozzo, R. / Gervasio, F. / Scapozza, L.
#1: Journal: Structure / Year: 2007
Title: c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty.
Authors: Seeliger, M.A. / Nagar, B. / Frank, F. / Cao, X. / Henderson, M.N. / Kuriyan, J.
#2: Journal: Chem.Biol. / Year: 2008
Title: Small molecule recognition of c-Src via the Imatinib-binding conformation.
Authors: Dar, A.C. / Lopez, M.S. / Shokat, K.M.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)66,3644
Polymers65,4532
Non-polymers9112
Water1,982110
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1822
Polymers32,7271
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1822
Polymers32,7271
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.268, 63.495, 73.451
Angle α, β, γ (deg.)79.48, 90.09, 89.41
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 319:328 )
211CHAIN B AND (RESSEQ 319:328 )
112CHAIN A AND (RESSEQ 336:384 )
212CHAIN B AND (RESSEQ 336:384 )
113CHAIN A AND (RESSEQ 386:403 )
213CHAIN B AND (RESSEQ 386:403 )
114CHAIN A AND (RESSEQ 424:533 )
214CHAIN B AND (RESSEQ 424:533 )

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 32726.645 Da / Num. of mol.: 2 / Mutation: L317I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PD5 / 1-{4-[4-amino-1-(1-methylethyl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]phenyl}-3-[3-(trifluoromethyl)phenyl]urea / 1-(4-(4-amino-1-isopropyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl)phenyl)-3-(3-(trifluoromethyl)phenyl)urea


Mass: 455.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20F3N7O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7mg/ml cSRcL317I, 0.5mM pyrazolopyrimidine 5, 0.1M MES, 0.2M sodium acetate, 4% glycerol, 12% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→32.945 Å / Num. obs: 18749 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 52.9 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.117 / Net I/σ(I): 10.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.22 / Rsym value: 0.538 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OEZ

3oez


Resolution: 2.75→32.945 Å / SU ML: 0.35 / σ(F): 2.07 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 938 5 %
Rwork0.1924 --
obs0.1944 18749 96.07 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.249 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 39.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.5435 Å2-2.2016 Å2-2.474 Å2
2---7.5176 Å22.3592 Å2
3---3.9741 Å2
Refinement stepCycle: LAST / Resolution: 2.75→32.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 66 110 4209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054205
X-RAY DIFFRACTIONf_angle_d0.8255705
X-RAY DIFFRACTIONf_dihedral_angle_d15.6731575
X-RAY DIFFRACTIONf_chiral_restr0.055607
X-RAY DIFFRACTIONf_plane_restr0.004725
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A84X-RAY DIFFRACTIONPOSITIONAL
12B84X-RAY DIFFRACTIONPOSITIONAL0.019
21A387X-RAY DIFFRACTIONPOSITIONAL
22B387X-RAY DIFFRACTIONPOSITIONAL0.024
31A131X-RAY DIFFRACTIONPOSITIONAL
32B131X-RAY DIFFRACTIONPOSITIONAL0.021
41A898X-RAY DIFFRACTIONPOSITIONAL
42B898X-RAY DIFFRACTIONPOSITIONAL0.019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.89490.3321320.29212497X-RAY DIFFRACTION95
2.8949-3.07620.28031340.23372566X-RAY DIFFRACTION96
3.0762-3.31350.2521340.20382539X-RAY DIFFRACTION96
3.3135-3.64660.21291350.18272556X-RAY DIFFRACTION96
3.6466-4.17330.21511330.17822529X-RAY DIFFRACTION96
4.1733-5.25450.18851340.15822569X-RAY DIFFRACTION96
5.2545-32.94710.24261360.18582555X-RAY DIFFRACTION97

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