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- PDB-1y57: Structure of unphosphorylated c-Src in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 1y57
TitleStructure of unphosphorylated c-Src in complex with an inhibitor
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / Kinase structure / SH3 / SH2
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / negative regulation of focal adhesion assembly / BMP receptor binding / positive regulation of integrin activation / positive regulation of protein processing / Activated NTRK2 signals through FYN / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / regulation of vascular permeability / focal adhesion assembly / connexin binding / osteoclast development / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / signal complex assembly / positive regulation of small GTPase mediated signal transduction / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / EPH-Ephrin signaling / positive regulation of podosome assembly / positive regulation of lamellipodium morphogenesis / regulation of bone resorption / Ephrin signaling / Signal regulatory protein family interactions / odontogenesis / negative regulation of mitochondrial depolarization / podosome / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / oogenesis / Co-inhibition by CTLA4 / GP1b-IX-V activation signalling / EPHA-mediated growth cone collapse / Receptor Mediated Mitophagy / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / positive regulation of Notch signaling pathway / Signaling by EGFR / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / regulation of cell-cell adhesion / uterus development / PECAM1 interactions / Recycling pathway of L1 / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of heart rate by cardiac conduction / RHOU GTPase cycle / protein tyrosine kinase activator activity / RET signaling / signaling receptor activator activity / negative regulation of anoikis / FCGR activation / Long-term potentiation / positive regulation of epithelial cell migration / progesterone receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / EPH-ephrin mediated repulsion of cells / GAB1 signalosome / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / negative regulation of hippo signaling / bone resorption / negative regulation of protein-containing complex assembly / Nuclear signaling by ERBB4 / phospholipase binding / ephrin receptor binding / T cell costimulation / p38MAPK events / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / Integrin signaling / EPHB-mediated forward signaling / ionotropic glutamate receptor binding / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth / Downregulation of ERBB4 signaling / Downstream signal transduction
Similarity search - Function
SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. ...SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MPZ / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsCowan-Jacob, S.W. / Fendrich, G. / Manley, P.W. / Jahnke, W. / Fabbro, D. / Liebetanz, J. / Meyer, T.
CitationJournal: Structure / Year: 2005
Title: The Crystal Structure of a c-Src Complex in an Active Conformation Suggests Possible Steps in c-Src Activation
Authors: Cowan-Jacob, S.W. / Fendrich, G. / Manley, P.W. / Jahnke, W. / Fabbro, D. / Liebetanz, J. / Meyer, T.
History
DepositionDec 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5897
Polymers51,6301
Non-polymers9606
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.212, 106.212, 123.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsMonomer in solution

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Components

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


Mass: 51629.590 Da / Num. of mol.: 1 / Fragment: SH3 SH2 and KINASE domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12931, EC: 2.7.1.112
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPZ / 4-[(4-METHYLPIPERAZIN-1-YL)METHYL]-N-{3-[(4-PYRIDIN-3-YLPYRIMIDIN-2-YL)AMINO]PHENYL}BENZAMIDE / 4-[(4-METHYL-1-PIPERAZINYL)METHYL]-N-[3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]AMINO]PHENYL]-BENZAMIDE


Mass: 479.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H29N7O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, tris, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00799 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 29, 2002
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00799 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 55770 / Num. obs: 55642 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.357 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 2813 5.1 %RANDOM
Rwork0.18781 ---
all0.18909 52747 --
obs0.18909 52747 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.521 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.91→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 61 315 3976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213746
X-RAY DIFFRACTIONr_bond_other_d0.0020.023326
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9725082
X-RAY DIFFRACTIONr_angle_other_deg0.79337732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025451
X-RAY DIFFRACTIONr_chiral_restr0.0780.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024127
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02779
X-RAY DIFFRACTIONr_nbd_refined0.1920.2633
X-RAY DIFFRACTIONr_nbd_other0.240.23674
X-RAY DIFFRACTIONr_nbtor_other0.0790.22041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0660.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.223
X-RAY DIFFRACTIONr_mcbond_it1.132.52251
X-RAY DIFFRACTIONr_mcangle_it1.96233632
X-RAY DIFFRACTIONr_scbond_it2.84741495
X-RAY DIFFRACTIONr_scangle_it4.59161450
LS refinement shellResolution: 1.905→1.955 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.26 197
Rwork0.229 3692
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2814-0.1574-0.22280.6142-0.50870.82810.03650.09790.0850.02990.02290.0151-0.14810.0356-0.05940.0607-0.040.02340.0460.0060.074-16.15442.84254.529
21.08250.3025-0.2721.2697-0.67141.72830.0008-0.0023-0.02970.15880.10930.2510.0072-0.1707-0.110.07220.03990.05230.02250.03460.113-31.47161.43841.538
30.5129-0.0974-0.00341.37160.59691.1107-0.00320.0807-0.00170.06560.0915-0.054-0.03630.0911-0.08830.0262-0.03850.02090.0756-0.02480.070910.79135.51449.057
41.3044-0.4177-0.02820.3812-0.00760.61510.03660.1292-0.0188-0.0255-0.053-0.0104-0.0233-0.10980.01640.03510.0362-0.02350.074-0.02190.063210.52425.35925.477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA82 - 1471 - 66
2X-RAY DIFFRACTION1AA248 - 258167 - 177
3X-RAY DIFFRACTION2AA148 - 24767 - 166
4X-RAY DIFFRACTION3AA259 - 340178 - 259
5X-RAY DIFFRACTION4AA341 - 533260 - 452

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