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- PDB-8h7f: The crystal structure of human abl1 kinase domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 8h7f
TitleThe crystal structure of human abl1 kinase domain in complex with abl1-B-EBA
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE / Complex / inhibitor / lysine
Function / homology
Function and homology information


mitochondrial depolarization / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / negative regulation of ubiquitin-protein transferase activity / podocyte apoptotic process / regulation of postsynaptic specialization assembly / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of modification of synaptic structure ...mitochondrial depolarization / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / negative regulation of ubiquitin-protein transferase activity / podocyte apoptotic process / regulation of postsynaptic specialization assembly / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / positive regulation of extracellular matrix organization / neuropilin signaling pathway / neuropilin binding / regulation of cell motility / bubble DNA binding / positive regulation of establishment of T cell polarity / cellular response to dopamine / positive regulation of blood vessel branching / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / regulation of Cdc42 protein signal transduction / regulation of hematopoietic stem cell differentiation / syntaxin binding / regulation of axon extension / regulation of T cell differentiation / positive regulation of cell migration involved in sprouting angiogenesis / Myogenesis / HDR through Single Strand Annealing (SSA) / platelet-derived growth factor receptor-beta signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / myoblast proliferation / regulation of endocytosis / cardiac muscle cell proliferation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / associative learning / positive regulation of focal adhesion assembly / actin monomer binding / ephrin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of vasoconstriction / regulation of cell adhesion / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / negative regulation of double-strand break repair via homologous recombination / positive regulation of T cell migration / mismatch repair / ephrin receptor binding / positive regulation of stress fiber assembly / four-way junction DNA binding / ruffle / signal transduction in response to DNA damage / phosphotyrosine residue binding / positive regulation of substrate adhesion-dependent cell spreading / actin filament polymerization / positive regulation of endothelial cell migration / integrin-mediated signaling pathway / SH2 domain binding / response to endoplasmic reticulum stress / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein kinase C binding / protein modification process / regulation of autophagy / protein serine/threonine kinase activator activity / regulation of actin cytoskeleton organization / intrinsic apoptotic signaling pathway in response to DNA damage / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / positive regulation of fibroblast proliferation / non-membrane spanning protein tyrosine kinase activity / Regulation of actin dynamics for phagocytic cup formation / cellular response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / enzyme activator activity / autophagy / sequence-specific double-stranded DNA binding / kinase activity / Cyclin D associated events in G1 / actin filament binding / actin cytoskeleton / positive regulation of neuron apoptotic process / manganese ion binding / mitotic cell cycle / positive regulation of cytosolic calcium ion concentration / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / growth cone / nuclear membrane / RUNX1 regulates transcription of genes involved in differentiation of HSCs / actin cytoskeleton organization / cellular response to oxidative stress / protein tyrosine kinase activity / response to oxidative stress
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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-QEW / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4501342407 Å
AuthorsZhu, C.J. / Zhang, Z.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: 2-Ethynylbenzaldehyde-Based, Lysine-Targeting Irreversible Covalent Inhibitors for Protein Kinases and Nonkinases.
Authors: Chen, P. / Tang, G. / Zhu, C. / Sun, J. / Wang, X. / Xiang, M. / Huang, H. / Wang, W. / Li, L. / Zhang, Z.M. / Gao, L. / Yao, S.Q.
History
DepositionOct 20, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)64,9104
Polymers64,1252
Non-polymers7852
Water3,513195
1
A: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4552
Polymers32,0631
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4552
Polymers32,0631
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.5018, 104.976, 132.487
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 32062.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Production host: Escherichia coli (E. coli)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-QEW / 1-[6-(6-methoxyisoquinolin-7-yl)-1,3-benzothiazol-2-yl]-3-(2-oxidanylideneethyl)urea


Mass: 392.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5M (NH4)2 SO4, 0.1M HEPES (PH 7.0) and 4% v/v 1,3-Propanediol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.12→52.25 Å / Num. obs: 46218 / % possible obs: 99.94 % / Redundancy: 13.3 % / CC1/2: 0.996 / Net I/σ(I): 9.3
Reflection shellResolution: 2.12→2.196 Å / Num. unique obs: 46218 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
xia2data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W7Y

7w7y


Resolution: 2.4501342407→42.988490614 Å / SU ML: 0.250228162536 / Cross valid method: FREE R-VALUE / σ(F): 1.33784226734 / Phase error: 23.466388683
RfactorNum. reflection% reflection
Rfree0.234153850318 1997 6.72481142241 %
Rwork0.203775710345 27699 -
obs0.205814881714 29696 99.9192462988 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.8427698956 Å2
Refinement stepCycle: LAST / Resolution: 2.4501342407→42.988490614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4246 0 0 195 4441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003168359113974359
X-RAY DIFFRACTIONf_angle_d0.6835605074945921
X-RAY DIFFRACTIONf_chiral_restr0.0263211635032629
X-RAY DIFFRACTIONf_plane_restr0.00279036033654740
X-RAY DIFFRACTIONf_dihedral_angle_d13.48370980821560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4502-2.51140.2815016288331390.2430582607691920X-RAY DIFFRACTION99.9514563107
2.5114-2.57930.3207587765791420.237331712581962X-RAY DIFFRACTION99.9050332384
2.5793-2.65520.2628067393941390.235685086161937X-RAY DIFFRACTION99.9037536092
2.6552-2.74090.2547637110921400.2335460886631934X-RAY DIFFRACTION99.9036608863
2.7409-2.83880.2897353546131420.2209184518331973X-RAY DIFFRACTION99.9527410208
2.8388-2.95240.2843492652611410.2259543859581947X-RAY DIFFRACTION100
2.9524-3.08680.2536745083571420.2189398008271958X-RAY DIFFRACTION100
3.0868-3.24950.2155953046891400.2131123955521956X-RAY DIFFRACTION100
3.2495-3.4530.2692482894561430.2064471912611969X-RAY DIFFRACTION100
3.453-3.71940.2518906185551420.1957149698381994X-RAY DIFFRACTION100
3.7194-4.09350.1987443714781430.1919900078511986X-RAY DIFFRACTION99.8592870544
4.0935-4.68520.1853738570581440.1752521125512008X-RAY DIFFRACTION99.9535531816
4.6852-5.90040.2174431059731470.1872379817292017X-RAY DIFFRACTION99.9538106236
5.9004-42.980.2112878716771530.1952208443182138X-RAY DIFFRACTION99.6520226185

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