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- PDB-3k5v: Structure of Abl kinase in complex with imatinib and GNF-2 -

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Basic information

Entry
Database: PDB / ID: 3k5v
TitleStructure of Abl kinase in complex with imatinib and GNF-2
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE / kinase / ATP-binding / Nucleotide-binding / Oncogene / SH2 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation ...Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / transitional one stage B cell differentiation / regulation of cellular senescence / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / cerebellum morphogenesis / neuroepithelial cell differentiation / B cell proliferation involved in immune response / Regulation of actin dynamics for phagocytic cup formation / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of extracellular matrix organization / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / regulation of extracellular matrix organization / neuropilin binding / bubble DNA binding / Myogenesis / positive regulation of establishment of T cell polarity / activated T cell proliferation / positive regulation of blood vessel branching / proline-rich region binding / circulatory system development / regulation of Cdc42 protein signal transduction / mitogen-activated protein kinase binding / syntaxin binding / alpha-beta T cell differentiation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of dendrite development / regulation of axon extension / regulation of T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of cell-cell adhesion / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / cell leading edge / platelet-derived growth factor receptor signaling pathway / regulation of microtubule polymerization / Bergmann glial cell differentiation / B cell proliferation / myoblast proliferation / associative learning / negative regulation of long-term synaptic potentiation / negative regulation of cellular senescence / negative regulation of mitotic cell cycle / neuromuscular process controlling balance / signal transduction in response to DNA damage / negative regulation of BMP signaling pathway / positive regulation of focal adhesion assembly / canonical NF-kappaB signal transduction / cardiac muscle cell proliferation / BMP signaling pathway / phagocytosis / ephrin receptor signaling pathway / positive regulation of T cell migration / endothelial cell migration / negative regulation of double-strand break repair via homologous recombination / cellular response to transforming growth factor beta stimulus / negative regulation of endothelial cell apoptotic process / positive regulation of vasoconstriction / four-way junction DNA binding / spleen development / positive regulation of stress fiber assembly / ephrin receptor binding / ruffle / ERK1 and ERK2 cascade / actin filament polymerization / phosphotyrosine residue binding / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of interleukin-2 production / substrate adhesion-dependent cell spreading / SH2 domain binding / positive regulation of mitotic cell cycle / protein kinase C binding / response to endoplasmic reticulum stress / positive regulation of release of sequestered calcium ion into cytosol / thymus development / integrin-mediated signaling pathway / post-embryonic development / B cell receptor signaling pathway / regulation of actin cytoskeleton organization / neural tube closure / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / enzyme activator activity / establishment of localization in cell
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 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 / 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-STI / Chem-STJ / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.74 Å
AuthorsCowan-Jacob, S.W. / Fendrich, G. / Rummel, G. / Strauss, A.
CitationJournal: Nature / Year: 2010
Title: Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors.
Authors: Zhang, J. / Adrian, F.J. / Jahnke, W. / Cowan-Jacob, S.W. / Li, A.G. / Iacob, R.E. / Sim, T. / Powers, J. / Dierks, C. / Sun, F. / Guo, G.R. / Ding, Q. / Okram, B. / Choi, Y. / ...Authors: Zhang, J. / Adrian, F.J. / Jahnke, W. / Cowan-Jacob, S.W. / Li, A.G. / Iacob, R.E. / Sim, T. / Powers, J. / Dierks, C. / Sun, F. / Guo, G.R. / Ding, Q. / Okram, B. / Choi, Y. / Wojciechowski, A. / Deng, X. / Liu, G. / Fendrich, G. / Strauss, A. / Vajpai, N. / Grzesiek, S. / Tuntland, T. / Liu, Y. / Bursulaya, B. / Azam, M. / Manley, P.W. / Engen, J.R. / Daley, G.Q. / Warmuth, M. / Gray, N.S.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1
B: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2587
Polymers67,4872
Non-polymers1,7715
Water7,728429
1
A: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6474
Polymers33,7441
Non-polymers9033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6113
Polymers33,7441
Non-polymers8682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.070, 65.268, 66.259
Angle α, β, γ (deg.)72.82, 80.25, 84.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Proto-oncogene c-Abl / p150


Mass: 33743.523 Da / Num. of mol.: 2 / Fragment: Kinase domain (UNP residues 229 to 515)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abl, Abl1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00520, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-STJ / 3-(6-{[4-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)benzamide


Mass: 374.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H13F3N4O2
#3: Chemical ChemComp-STI / 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE / STI-571 / IMATINIB


Mass: 493.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31N7O / Comment: medication, inhibitor*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M MES pH 5.6, 0.2 M MgCl2, 18 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0016 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0016 Å / Relative weight: 1
ReflectionResolution: 1.74→62.5 Å / Num. all: 64929 / Num. obs: 64929 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.045 / Net I/σ(I): 16.5
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.382 / % possible all: 86.2

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Processing

Software
NameVersionClassification
MAR345CCD softwaredata collection
REFMAC5.5.0063refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.0063phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1OPJ

1opj


Resolution: 1.74→38.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.335 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23117 3247 5 %RANDOM
Rwork0.19899 ---
all0.20062 61682 --
obs0.20062 61682 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20.03 Å20.49 Å2
2--0.3 Å2-0.43 Å2
3---0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.121 Å0.127 Å
Refinement stepCycle: LAST / Resolution: 1.74→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 129 429 5178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224895
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.996631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01524.439223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94915847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1071522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213726
X-RAY DIFFRACTIONr_mcbond_it1.04322849
X-RAY DIFFRACTIONr_mcangle_it1.9134603
X-RAY DIFFRACTIONr_scbond_it2.16542046
X-RAY DIFFRACTIONr_scangle_it3.27352026
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 211 -
Rwork0.264 4011 -
obs-4011 83.82 %

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