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- PDB-1fpu: CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MO... -

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Basic information

Entry
Database: PDB / ID: 1fpu
TitleCRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MOLECULE INHIBITOR
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
KeywordsTRANSFERASE / kinase / kinase inhibitor / STI-571 / activation loop
Function / homology
Function and homology information


Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Cyclin D associated events in G1 / HDR through Single Strand Annealing (SSA) / Myogenesis / RHO GTPases Activate WASPs and WAVEs / Role of ABL in ROBO-SLIT signaling / Regulation of actin dynamics for phagocytic cup formation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / delta-catenin binding / transitional one stage B cell differentiation ...Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Cyclin D associated events in G1 / HDR through Single Strand Annealing (SSA) / Myogenesis / RHO GTPases Activate WASPs and WAVEs / Role of ABL in ROBO-SLIT signaling / Regulation of actin dynamics for phagocytic cup formation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / delta-catenin binding / transitional one stage B cell differentiation / positive regulation of actin filament binding / activation of protein kinase C activity / DNA conformation change / negative regulation of phospholipase C activity / actin filament branching / positive regulation of interleukin-2 secretion / positive regulation blood vessel branching / B cell proliferation involved in immune response / positive regulation of microtubule binding / neuroepithelial cell differentiation / regulation of extracellular matrix organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / regulation of modification of synaptic structure / cerebellum morphogenesis / collateral sprouting / B-1 B cell homeostasis / cardiovascular system development / positive regulation of oxidoreductase activity / alpha-beta T cell differentiation / activated T cell proliferation / bubble DNA binding / B cell proliferation / neuropilin signaling pathway / neuropilin binding / regulation of T cell differentiation / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / negative regulation of ubiquitin-protein transferase activity / regulation of microtubule polymerization / negative regulation of BMP signaling pathway / mitogen-activated protein kinase binding / sequence-specific double-stranded DNA binding / regulation of cellular senescence / proline-rich region binding / positive regulation of interferon-gamma secretion / syntaxin binding / negative regulation of cell-cell adhesion / regulation of response to DNA damage stimulus / DNA damage induced protein phosphorylation / negative regulation of cellular senescence / platelet-derived growth factor receptor signaling pathway / positive regulation of osteoblast proliferation / cell leading edge / regulation of axon extension / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of long-term synaptic potentiation / neuromuscular process controlling balance / Bergmann glial cell differentiation / positive regulation of focal adhesion assembly / positive regulation of actin cytoskeleton reorganization / negative regulation of mitotic cell cycle / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / phagocytosis / negative regulation of endothelial cell apoptotic process / endothelial cell migration / positive regulation of stress fiber assembly / regulation of actin cytoskeleton organization / signal transduction in response to DNA damage / substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / spleen development / SH2 domain binding / post-embryonic development / neural tube closure / negative regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of mitotic cell cycle / ruffle / positive regulation of release of sequestered calcium ion into cytosol / thymus development / protein kinase C binding / negative regulation of ERK1 and ERK2 cascade / phosphotyrosine residue binding / neuron differentiation / ephrin receptor binding / integrin-mediated signaling pathway / actin cytoskeleton organization / autophagy / regulation of cell cycle / non-specific protein-tyrosine kinase / peptidyl-tyrosine autophosphorylation / epidermal growth factor receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / establishment of protein localization / actin cytoskeleton / SH3 domain binding / cellular response to hydrogen peroxide / positive regulation of neuron death
SH2 domain / Tyrosine-protein kinase ABL, SH2 domain / Protein kinases ATP-binding region signature. / F-actin binding / Protein kinase domain / SH3 domain / SH2 domain / SH2 domain superfamily / SH3-like domain superfamily / Tyrosine-protein kinase ABL1/transforming protein Abl ...SH2 domain / Tyrosine-protein kinase ABL, SH2 domain / Protein kinases ATP-binding region signature. / F-actin binding / Protein kinase domain / SH3 domain / SH2 domain / SH2 domain superfamily / SH3-like domain superfamily / Tyrosine-protein kinase ABL1/transforming protein Abl / Src homology 2 (SH2) domain profile. / Tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / F-actin binding / Protein kinase-like domain superfamily / Tyrosine-protein kinase, active site / SH3 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Protein tyrosine kinase / Src homology 3 (SH3) domain profile. / Protein kinase domain profile.
Tyrosine-protein kinase ABL1
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsSchindler, T. / Bornmann, W. / Pellicena, P. / Miller, W.T. / Clarkson, B. / Kuriyan, J.
CitationJournal: Science / Year: 2000
Title: Structural mechanism for STI-571 inhibition of abelson tyrosine kinase.
Authors: Schindler, T. / Bornmann, W. / Pellicena, P. / Miller, W.T. / Clarkson, B. / Kuriyan, J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
B: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2524
Polymers67,4872
Non-polymers7652
Water1,78399
1
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1262
Polymers33,7441
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1262
Polymers33,7441
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)110.7, 146.1, 152.8
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
DetailsThere are two kinase molecules in the asymmetric unit. The biological assembly is a monomer.

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Components

#1: Protein/peptide PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL / P150 / C-ABL


Mass: 33743.523 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00520, EC: 2.7.1.112
#2: Chemical ChemComp-PRC / N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]AMINO]PHENYL]-3-PYRIDINECARBOXAMIDE


Mass: 382.418 Da / Num. of mol.: 2 / Fragment: 2-(PHENYLAMINO)-PYRIMIDINE COMPOUND / Source method: obtained synthetically / Formula: C22H18N6O
Details: chemically synthesized as described in Zimmermann J., Buchdunger E., Mett H., Meyer T., Lydon N.B. (1997) Bioorg. Med. Chem. Lett., Vol. 7, pp. 187
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, magnesium chloride, mes, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDChemical formula
120 mMTris-HCldrop
2100 mMdropNaCl
33 mMdithiothreitoldrop
430 mg/mlproteindrop
525 %(w/v)PEG4000reservoir
6100 mMMES- NaOHreservoir
70.2 MreservoirMgCl2

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9393
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. obs: 221636 / % possible obs: 98.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.216 / Num. unique all: 2190 / % possible all: 90.6
Reflection
*PLUS
Num. obs: 24122 / Num. measured all: 221636
Reflection shell
*PLUS
% possible obs: 90.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.4→99 Å / Stereochemistry target values: Engh & Huber
Details: Tight, noncrystallographic restraints were utilized throughout the refinement so that the final r.m.s. deviation between the two molecules is 0.05 and 0.04 Angstrom for the N-terminal and the C-terminal lobes, respectively (excluding residues 229 to 337, 252, 262, 271, 294, 306, 404, 447, 450, 466, and 491, which were built in different conformations in the two molecules). The electron density map was significantly weaker for one of the two molecules in the asymmetric unit (chain ID B), and all the analysis (cf. primary citation) relied on the better-ordered one (chain ID A).
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2383 -random
Rwork0.239 ---
All-24658 --
Obs-24122 97.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 58 99 4451
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 99 Å / Rfactor obs: 0.239
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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