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- PDB-1yom: Crystal structure of Src kinase domain in complex with Purvalanol A -

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Basic information

Entry
Database: PDB / ID: 1yom
TitleCrystal structure of Src kinase domain in complex with Purvalanol A
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / protein tyrosine kinase
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / negative regulation of telomere maintenance / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / negative regulation of telomere maintenance / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / positive regulation of dephosphorylation / regulation of epithelial cell migration / ERBB2 signaling pathway / positive regulation of protein transport / Regulation of gap junction activity / cellular response to progesterone stimulus / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / positive regulation of integrin activation / Activated NTRK2 signals through FYN / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / regulation of vascular permeability / negative regulation of neutrophil activation / positive regulation of glucose metabolic process / transcytosis / osteoclast development / Activated NTRK3 signals through PI3K / connexin binding / focal adhesion assembly / cellular response to fluid shear stress / adherens junction organization / signal complex assembly / positive regulation of small GTPase mediated signal transduction / Co-stimulation by CD28 / branching involved in mammary gland duct morphogenesis / response to acidic pH / positive regulation of Ras protein signal transduction / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / positive regulation of podosome assembly / EPH-Ephrin signaling / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / myoblast proliferation / Signal regulatory protein family interactions / cellular response to peptide hormone stimulus / negative regulation of mitochondrial depolarization / podosome / odontogenesis / MET activates PTK2 signaling / cellular response to fatty acid / Regulation of KIT signaling / postsynaptic specialization, intracellular component / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / oogenesis / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / EPHA-mediated growth cone collapse / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / DNA biosynthetic process / positive regulation of Notch signaling pathway / Signaling by EGFR / stress fiber assembly / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / uterus development / regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / PECAM1 interactions / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / dendritic growth cone / protein tyrosine kinase activator activity / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / negative regulation of anoikis / RET signaling / Long-term potentiation / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / GAB1 signalosome / positive regulation of protein serine/threonine kinase activity / negative regulation of hippo signaling
Similarity search - Function
: / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...: / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / 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 / 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 Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-P01 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBreitenlechner, C.B. / Kairies, N.A. / Honold, K. / Scheiblich, S. / Koll, H. / Greiter, E. / Koch, S. / Schaefer, W. / Huber, R. / Engh, R.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of active SRC kinase domain complexes
Authors: Breitenlechner, C.B. / Kairies, N.A. / Honold, K. / Scheiblich, S. / Koll, H. / Greiter, E. / Koch, S. / Schaefer, W. / Huber, R. / Engh, R.A.
History
DepositionJan 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4May 29, 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)65,6784
Polymers64,9002
Non-polymers7782
Water2,234124
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8392
Polymers32,4501
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8392
Polymers32,4501
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.698, 63.078, 74.055
Angle α, β, γ (deg.)100.61, 88.86, 89.89
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 32450.248 Da / Num. of mol.: 2 / Fragment: Src kinase domain / Mutation: S344N, A369S, Y418W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P12931, EC: 2.7.1.112
#2: Chemical ChemComp-P01 / 2-({6-[(3-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL / PURVALANOL A


Mass: 388.894 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25ClN6O / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% ethylene glycol , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 31, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.7→21.8 Å / Num. all: 18966 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.123 / Net I/σ(I): 4.6
Reflection shellResolution: 2.7→2.85 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.469 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→12 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.811 / SU B: 19.723 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31322 742 4.9 %RANDOM
Rwork0.21704 ---
obs0.22187 14312 92.88 %-
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: 44.857 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å21.3 Å2-0.11 Å2
2---1.81 Å2-0.1 Å2
3---5.08 Å2
Refinement stepCycle: LAST / Resolution: 2.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 54 124 4347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224340
X-RAY DIFFRACTIONr_bond_other_d0.0020.023951
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9845884
X-RAY DIFFRACTIONr_angle_other_deg0.91239202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7415517
X-RAY DIFFRACTIONr_chiral_restr0.080.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024734
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02856
X-RAY DIFFRACTIONr_nbd_refined0.2190.21051
X-RAY DIFFRACTIONr_nbd_other0.2220.24799
X-RAY DIFFRACTIONr_nbtor_other0.0860.22556
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.24
X-RAY DIFFRACTIONr_mcbond_it0.6381.52601
X-RAY DIFFRACTIONr_mcangle_it1.18824204
X-RAY DIFFRACTIONr_scbond_it1.25331739
X-RAY DIFFRACTIONr_scangle_it2.1964.51680
LS refinement shellResolution: 2.9→2.971 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.442 55
Rwork0.247 1056

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