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- PDB-3ms9: ABL kinase in complex with imatinib and a fragment (FRAG1) in the... -

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Basic information

Entry
Database: PDB / ID: 3ms9
TitleABL kinase in complex with imatinib and a fragment (FRAG1) in the myristate pocket
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / kinase / fragment-based screening / FBS / TRANSFERASE / TRANSFERASE-TRANSFERASE REGULATOR complex
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 / DN4 thymocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs ...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 / 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 / DNA conformation change / neuroepithelial cell differentiation / B cell proliferation involved in immune response / Regulation of actin dynamics for phagocytic cup formation / cerebellum morphogenesis / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of extracellular matrix organization / microspike assembly / circulatory system development / B-1 B cell homeostasis / regulation of extracellular matrix organization / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / Myogenesis / activated T cell proliferation / positive regulation of establishment of T cell polarity / positive regulation of blood vessel branching / proline-rich region binding / regulation of Cdc42 protein signal transduction / syntaxin binding / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / positive regulation of dendrite development / regulation of axon extension / regulation of T cell differentiation / cardiac muscle cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of cell-cell adhesion / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of osteoblast proliferation / cell leading edge / regulation of microtubule polymerization / associative learning / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / B cell proliferation / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / negative regulation of mitotic cell cycle / negative regulation of cellular senescence / negative regulation of BMP signaling pathway / ephrin receptor signaling pathway / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / phagocytosis / BMP signaling pathway / endothelial cell migration / positive regulation of T cell migration / negative regulation of double-strand break repair via homologous recombination / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / cellular response to transforming growth factor beta stimulus / spleen development / positive regulation of stress fiber assembly / ruffle / positive regulation of vasoconstriction / ephrin receptor binding / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / SH2 domain binding / response to endoplasmic reticulum stress / positive regulation of release of sequestered calcium ion into cytosol / thymus development / protein kinase C binding / post-embryonic development / integrin-mediated signaling pathway / establishment of localization in cell / non-membrane spanning protein tyrosine kinase activity / regulation of actin cytoskeleton organization / B cell receptor signaling pathway / neural tube closure / non-specific protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade
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 / 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
methyl 2-amino-4-chlorobenzoate / Chem-STI / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsCowan-Jacob, S.W. / Rummel, G. / Fendrich, G.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Binding or bending: distinction of allosteric Abl kinase agonists from antagonists by an NMR-based conformational assay.
Authors: Jahnke, W. / Grotzfeld, R.M. / Pelle, X. / Strauss, A. / Fendrich, G. / Cowan-Jacob, S.W. / Cotesta, S. / Fabbro, D. / Furet, P. / Mestan, J. / Marzinzik, A.L.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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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)69,05812
Polymers67,4872
Non-polymers1,57110
Water7,981443
1
A: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5657
Polymers33,7441
Non-polymers8216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4945
Polymers33,7441
Non-polymers7504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.783, 147.346, 152.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-148-

HOH

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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, residues 229-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abl1, Abl / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00520, non-specific protein-tyrosine kinase
#2: 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
#3: Chemical ChemComp-MS9 / methyl 2-amino-4-chlorobenzoate


Mass: 185.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8ClNO2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: protein concentration: 20mg/ml. Crystallisation buffer: 0.1M MES pH 6.5, 0.2M MgCl2, 18.4% PEG4000, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→33.92 Å / Num. all: 58848 / Num. obs: 58848 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.38
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.58 / Num. unique all: 6016 / % possible all: 83.3

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Processing

Software
NameClassification
MAR345dtbdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→33.92 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.524 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23391 2942 5 %RANDOM
Rwork0.18552 ---
obs0.18794 55882 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.212 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2---0.84 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4359 0 104 443 4906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224635
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9786285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91224.206214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35715787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4981522
X-RAY DIFFRACTIONr_chiral_restr0.1610.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213548
X-RAY DIFFRACTIONr_mcbond_it1.4361.52708
X-RAY DIFFRACTIONr_mcangle_it2.4124373
X-RAY DIFFRACTIONr_scbond_it3.43531927
X-RAY DIFFRACTIONr_scangle_it5.3634.51909
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 178 -
Rwork0.349 3376 -
obs--81.63 %

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