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- PDB-2g2i: A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 2g2i
TitleA Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain
Components
  • ATP-Peptide Conjugate
  • Abl Tyrosine Kinase
KeywordsTRANSFERASE / Protein Kinase
Function / homology
Function and homology information


: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation ...: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / neuropilin signaling pathway / negative regulation of ubiquitin-protein transferase activity / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / syntaxin binding / regulation of hematopoietic stem cell differentiation / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / Myogenesis / positive regulation of osteoblast proliferation / regulation of microtubule polymerization / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / negative regulation of mitotic cell cycle / actin monomer binding / negative regulation of BMP signaling pathway / negative regulation of long-term synaptic potentiation / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / signal transduction in response to DNA damage / BMP signaling pathway / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / mismatch repair / negative regulation of endothelial cell apoptotic process / canonical NF-kappaB signal transduction / four-way junction DNA binding / peptidyl-tyrosine autophosphorylation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / ruffle / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization / phosphotyrosine residue binding / positive regulation of endothelial cell migration / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / SH2 domain binding / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / regulation of autophagy / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
ADENOSINE-5'-DIPHOSPHATE / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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 16, 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,2766
Polymers69,4214
Non-polymers8542
Water00
1
A: Abl Tyrosine Kinase
C: ATP-Peptide Conjugate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1383
Polymers34,7112
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-9 kcal/mol
Surface area14190 Å2
MethodPISA
2
B: Abl Tyrosine Kinase
D: ATP-Peptide Conjugate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1383
Polymers34,7112
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-12 kcal/mol
Surface area13800 Å2
MethodPISA
3
A: Abl Tyrosine Kinase
B: Abl Tyrosine Kinase
C: ATP-Peptide Conjugate
D: ATP-Peptide Conjugate
hetero molecules

A: Abl Tyrosine Kinase
B: Abl Tyrosine Kinase
C: ATP-Peptide Conjugate
D: ATP-Peptide Conjugate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,55112
Polymers138,8428
Non-polymers1,7094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12790 Å2
ΔGint-75 kcal/mol
Surface area48630 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-31 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.457, 88.457, 235.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 33181.957 Da / Num. of mol.: 2 / Fragment: Abl Tyrosine 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: 1528.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid phase peptide synthesis
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.32 Å3/Da / Density % sol: 62.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M sodium malonate , pH 8.0, 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
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 17209 / Num. obs: 17209 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.2
Reflection shellResolution: 3.12→3.27 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.75 / % possible all: 95.1

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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: 3.12→50 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.308 867 random
Rwork0.249 --
all0.251 17057 -
obs0.251 17057 -
Refinement stepCycle: LAST / Resolution: 3.12→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 54 0 4518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.67

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