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- PDB-7w7y: The crystal structure of human abl1 kinase domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 7w7y
TitleThe crystal structure of human abl1 kinase domain in complex with ABL2-A5
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE / ABL1
Function / homology
Function and homology information


positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding ...positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / transitional one stage B cell differentiation / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / DNA conformation change / neuroepithelial cell differentiation / B cell proliferation involved in immune response / : / cerebellum morphogenesis / 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 / neuropilin binding / mitochondrial depolarization / bubble DNA binding / regulation of cell motility / positive regulation of establishment of T cell polarity / activated T cell proliferation / cellular response to dopamine / positive regulation of blood vessel branching / proline-rich region binding / regulation of Cdc42 protein signal transduction / syntaxin binding / mitogen-activated protein kinase binding / regulation of hematopoietic stem cell differentiation / 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 peptidyl-tyrosine phosphorylation / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / HDR through Single Strand Annealing (SSA) / Myogenesis / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / regulation of microtubule polymerization / associative learning / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / negative regulation of cellular senescence / negative regulation of mitotic cell cycle / negative regulation of BMP signaling pathway / actin monomer binding / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / RHO GTPases Activate WASPs and WAVEs / BMP signaling pathway / endothelial cell migration / positive regulation of T cell migration / negative regulation of double-strand break repair via homologous recombination / mismatch repair / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / peptidyl-tyrosine autophosphorylation / 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 / positive regulation of endothelial cell migration / 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 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein kinase C binding / post-embryonic development / integrin-mediated signaling pathway / 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 / 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 / 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-8IW / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20003021871 Å
AuthorsZhu, C. / Zhang, Z.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Cell-Active, Reversible, and Irreversible Covalent Inhibitors That Selectively Target the Catalytic Lysine of BCR-ABL Kinase.
Authors: Chen, P. / Sun, J. / Zhu, C. / Tang, G. / Wang, W. / Xu, M. / Xiang, M. / Zhang, C.J. / Zhang, Z.M. / Gao, L. / Yao, S.Q.
History
DepositionDec 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 29, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 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

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)64,9564
Polymers64,1232
Non-polymers8332
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area24260 Å2
Unit cell
Length a, b, c (Å)56.519, 105.348, 132.275
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,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-838-

HOH

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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: 32061.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-8IW / 5-[3-(5-methanoyl-2-methoxy-4-oxidanyl-phenyl)-1~{H}-pyrrolo[2,3-b]pyridin-5-yl]-~{N},~{N}-dimethyl-pyridine-3-carboxamide


Mass: 416.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 60.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5 M (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: BL17B1 / Wavelength: 0.9876 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9876 Å / Relative weight: 1
ReflectionResolution: 2.2→42.97 Å / Num. obs: 40910 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.4
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 4020 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
autoPROCdata processing
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GQG

2gqg


Resolution: 2.20003021871→42.9670398702 Å / SU ML: 0.222783145761 / Cross valid method: FREE R-VALUE / σ(F): 1.3434868188 / Phase error: 20.0211556575
RfactorNum. reflection% reflection
Rfree0.201239799431 2052 5.01711491443 %
Rwork0.174910741354 38848 -
obs0.176239907134 40900 99.958452477 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4462999786 Å2
Refinement stepCycle: LAST / Resolution: 2.20003021871→42.9670398702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 60 384 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007480139859914475
X-RAY DIFFRACTIONf_angle_d1.125175831426074
X-RAY DIFFRACTIONf_chiral_restr0.046429874879642
X-RAY DIFFRACTIONf_plane_restr0.00452452791241761
X-RAY DIFFRACTIONf_dihedral_angle_d17.50222468831628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25120.2240011168221300.1975077241392548X-RAY DIFFRACTION100
2.2512-2.30750.2866654148251410.1921529922512524X-RAY DIFFRACTION100
2.3075-2.36990.2591057994311280.1914833492572572X-RAY DIFFRACTION100
2.3699-2.43960.2416894188861380.1926534893942568X-RAY DIFFRACTION99.9630587366
2.4396-2.51830.2202175888441380.1930274550032529X-RAY DIFFRACTION100
2.5183-2.60830.2190416144761510.1990567185012547X-RAY DIFFRACTION100
2.6083-2.71280.2331378872661440.1826075643912591X-RAY DIFFRACTION100
2.7128-2.83620.2615504461371240.1919824741092559X-RAY DIFFRACTION100
2.8362-2.98570.2133465187411440.1896220636242574X-RAY DIFFRACTION100
2.9857-3.17270.2588262448781300.1909260141222578X-RAY DIFFRACTION100
3.1727-3.41760.1923664622421250.1769352718932605X-RAY DIFFRACTION100
3.4176-3.76130.1821722940161570.1612022551262598X-RAY DIFFRACTION99.9637155298
3.7613-4.30520.1758585236981340.1437579841872605X-RAY DIFFRACTION100
4.3052-5.42230.15269071881520.1492723751422642X-RAY DIFFRACTION100
5.4223-42.960.1651268965151160.1856706206972808X-RAY DIFFRACTION99.5573714675
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)
13.25845865069-1.09816011353-0.1146777913872.378057964790.7568208454342.406006847060.105014234924-0.01978063744540.174681252074-0.364820009104-0.2145358876180.320764527574-0.0319797913234-0.2845115168360.1033802725130.245778398789-0.0197527141736-0.03464553494250.292169680175-0.0767963079090.342112024488-29.59431.183-20.54
21.870876036050.0515877203209-0.02519110634841.397270445670.3149281245041.373523438550.0331506657870.086711139941-0.166525976663-0.0130643311676-0.0494723725401-0.0168347841020.03613660110370.00925058055469-0.00477533822710.160609194318-0.00469368946524-0.00255502794710.143224984199-0.01432467197390.14636011785-9.05434.556-10.969
36.69190179519-0.2461338065880.02146311217675.965509962220.9138993809928.53368752375-0.142265109458-0.819398875491-0.3858722346711.006323886970.05698766578560.0251863812650.687636386706-0.2442242524980.09239032223670.297799591936-0.009780673801670.001101711041450.2162834818180.06602819095310.266290452397-7.53929.0654.507
42.649508150830.630689620266-0.02169685493791.75473363782-0.9699776759992.28477417989-0.1452032452810.6162014414640.632782700474-0.6024024775380.0540337516958-0.0321285266824-0.7215438431260.03969727617530.1255300455660.758759992307-0.0170503421347-0.015304721740.4067284566290.04760575420470.516267592678-17.67235.39-55.029
52.28483900456-0.1251198624310.4226456619681.767651892890.08791386827971.37705336999-0.1253694327270.1621630863050.238910079346-0.2136472184810.0589179104009-0.0906580662607-0.4050050651740.1211597198520.05244665743680.3551221135150.00569578807232-0.002342349599710.26674145654-0.06751160938790.277838883158-14.1125.789-44.142
63.521395094280.5583939908030.8688354032391.925876510440.4341472293661.87638251308-0.107853006940.4708854577590.164883147048-0.3974572746760.09330112008570.0961588051351-0.2199487865980.07799953884390.04845403255960.3277154629760.0157814790415-0.02362422205040.326589312473-0.02878523220610.248188505718-21.50819.964-51.742
71.62088728125-0.96929053852-0.3849997875312.226797659670.3887435643561.243880539510.1198702106530.112679306107-0.148041645116-0.0906687014314-0.08652859867860.09688077862750.03594971784820.0973740112822-0.03557601850130.1825333853170.0320328083942-0.03471319450120.251199864043-0.07339486588790.244947802449-15.8486.501-45.068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 232:292 )A232 - 292
2X-RAY DIFFRACTION2( CHAIN A AND RESID 293:485 )A293 - 485
3X-RAY DIFFRACTION3( CHAIN A AND RESID 486:500 )A486 - 500
4X-RAY DIFFRACTION4( CHAIN B AND RESID 232:300 )B232 - 300
5X-RAY DIFFRACTION5( CHAIN B AND RESID 301:356 )B301 - 356
6X-RAY DIFFRACTION6( CHAIN B AND RESID 357:400 )B357 - 400
7X-RAY DIFFRACTION7( CHAIN B AND RESID 401:500 )B401 - 500

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