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- PDB-2g2f: A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 2g2f
TitleA Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain
Components
  • ATP-Peptide Conjugate
  • Abl Kinase
KeywordsTRANSFERASE / protein kinase
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 / regulation of T cell differentiation / 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 / 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 / cellular response to transforming growth factor beta stimulus / ephrin receptor signaling pathway / positive regulation of vasoconstriction / regulation of cell adhesion / positive regulation of substrate adhesion-dependent cell spreading / endothelial cell migration / positive regulation of stress fiber assembly / 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 / four-way junction DNA binding / ruffle / signal transduction in response to DNA damage / phosphotyrosine residue binding / actin filament polymerization / positive regulation of endothelial cell migration / SH2 domain binding / integrin-mediated signaling pathway / protein serine/threonine kinase activator activity / positive regulation of fibroblast proliferation / 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 actin cytoskeleton organization / intrinsic apoptotic signaling pathway in response to DNA damage / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / regulation of autophagy / Regulation of actin dynamics for phagocytic cup formation / cellular response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / enzyme activator activity / autophagy / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / kinase activity / Cyclin D associated events in G1 / actin filament binding / actin cytoskeleton organization / actin cytoskeleton / manganese ion binding / mitotic cell cycle / positive regulation of cytosolic calcium ion concentration / nuclear membrane / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to oxidative stress / protein tyrosine kinase activity / cellular 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 / 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-112 / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLevinson, N.M. / Kuchment, O.
CitationJournal: Plos Biol. / Year: 2006
Title: A SRC-like inactive conformation in the abl tyrosine kinase domain.
Authors: Levinson, N.M. / Kuchment, O. / Shen, K. / Young, M.A. / Koldobskiy, M. / Karplus, M. / Cole, P.A. / Kuriyan, J.
History
DepositionFeb 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2012Group: Non-polymer description
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abl Kinase
B: Abl Kinase
C: ATP-Peptide Conjugate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6625
Polymers67,5583
Non-polymers1,1042
Water1,53185
1
A: Abl Kinase
C: ATP-Peptide Conjugate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9573
Polymers34,3762
Non-polymers5801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-11 kcal/mol
Surface area14040 Å2
MethodPISA
2
B: Abl Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7052
Polymers33,1821
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.669, 133.322, 56.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Abl Kinase / p150 / c- ABL / Abelson murine leukemia viral oncogene homolog 1


Mass: 33181.957 Da / Num. of mol.: 2 / Fragment: Abl Kinase Domain / Mutation: H396P
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
#2: Protein/peptide ATP-Peptide Conjugate


Mass: 1194.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-112 / THIOPHOSPHORIC ACID O-((ADENOSYL-PHOSPHO)PHOSPHO)-S-ACETAMIDYL-DIESTER


Mass: 580.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N6O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.115879 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 22582 / Num. obs: 22582 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.11 / Net I/σ(I): 10.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.05 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M52

1m52


Resolution: 2.7→50 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.286 1115 random
Rwork0.232 --
all0.234 22582 -
obs0.234 22582 -
Displacement parametersBiso mean: 52.8 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4435 0 66 85 4586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0087
X-RAY DIFFRACTIONc_angle_deg1.37

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