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- PDB-5np2: Abl1 SH3 pTyr89/134 -

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Basic information

Entry
Database: PDB / ID: 5np2
TitleAbl1 SH3 pTyr89/134
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE / signaling / tyrosine phosphorylation / SH3 domain / 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 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMero, B. / Radnai, L. / Gogl, G. / Leveles, I. / Buday, L.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural insights into the tyrosine phosphorylation-mediated inhibition of SH3 domain-ligand interactions.
Authors: Mero, B. / Radnai, L. / Gogl, G. / Toke, O. / Leveles, I. / Koprivanacz, K. / Szeder, B. / Dulk, M. / Kudlik, G. / Vas, V. / Cserkaszky, A. / Sipeki, S. / Nyitray, L. / Vertessy, B.G. / Buday, L.
History
DepositionApr 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)13,8192
Polymers13,8192
Non-polymers00
Water1,31573
1
A: Tyrosine-protein kinase ABL1


Theoretical massNumber of molelcules
Total (without water)6,9091
Polymers6,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase ABL1


Theoretical massNumber of molelcules
Total (without water)6,9091
Polymers6,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.630, 83.180, 57.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-218-

HOH

21B-226-

HOH

31B-242-

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: 6909.432 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.8 M sodium citrate, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→41.59 Å / Num. obs: 15844 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.039 / Net I/σ(I): 22.97
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 6.75 % / Mean I/σ(I) obs: 2.61 / Num. unique obs: 1135 / CC1/2: 0.815 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1750refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABO

1abo


Resolution: 1.6→41.59 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.2219 775 4.9 %
Rwork0.1891 --
obs0.1908 15825 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 0 73 1012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011005
X-RAY DIFFRACTIONf_angle_d1.3091381
X-RAY DIFFRACTIONf_dihedral_angle_d15.203346
X-RAY DIFFRACTIONf_chiral_restr0.055141
X-RAY DIFFRACTIONf_plane_restr0.007177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.70030.2991280.2512454X-RAY DIFFRACTION100
1.7003-1.83160.2771030.23682488X-RAY DIFFRACTION100
1.8316-2.01590.29561140.20622507X-RAY DIFFRACTION100
2.0159-2.30760.23861260.20142509X-RAY DIFFRACTION100
2.3076-2.90720.22171480.21082504X-RAY DIFFRACTION100
2.9072-41.6040.20011560.1642588X-RAY DIFFRACTION100
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)
15.98811.3933-2.554.2426-0.7547.9978-0.0386-0.0426-0.04960.3348-0.07-0.24480.15930.26140.11780.19070.04920.03090.21370.02240.254212.26538.961311.2513
23.322-0.94983.64433.2906-0.13925.14320.0382-0.0218-0.6314-0.1715-0.00871.05520.2680.2354-0.10070.3131-0.01860.01040.2569-0.00820.4271.474514.92429.8662
33.8822-0.99330.77368.9108-1.18554.9691-0.17540.1257-0.10910.1662-0.0296-0.1380.05230.12260.10870.15560.00980.02530.2895-0.03040.23548.679712.361610.9983
42.0023-3.5161-5.69043.39070.64854.2028-0.6432-1.0321-0.7260.5853-0.68520.5061-0.2309-1.78241.04091.2649-0.31940.01381.0307-0.07480.4525-12.741832.78552.3098
58.65981.1540.33085.8404-0.60223.7579-0.3563-0.0953-0.1585-0.21110.2126-0.4393-0.15340.20760.17690.28410.02830.01280.14650.00010.23746.044535.5260.6334
68.35530.1386-0.11553.2795-5.48219.2597-0.46410.0281.6260.0562-0.4085-0.7739-1.05550.71620.90180.48270.0359-0.03190.52980.23740.707911.381321.047-0.2791
72.2571-2.06820.43043.4649-2.63643.3910.2345-0.0897-0.0865-0.9534-0.0489-0.61410.27480.2808-0.06510.39370.01310.05340.27130.02180.31836.107731.8732-3.5622
80.7583-1.00911.5122.4518-2.45418.5371-0.04520.23160.0829-0.024-0.0017-0.0785-0.04030.41620.05770.1897-0.013-0.02180.2250.00520.1851.478727.04987.5748
96.09050.63165.83833.65810.90035.72060.34450.809-0.1404-0.1119-0.10230.01540.44820.7116-0.09450.23590.03730.00780.30660.01930.18222.524126.063-1.2632
102.9248-3.17971.31433.9361-1.4193.7390.18590.28680.87520.0691-0.4097-0.4325-0.30880.20460.11940.2942-0.0195-0.0310.27350.02750.29783.171136.05195.8685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 119 )
4X-RAY DIFFRACTION4chain 'B' and (resid 60 through 64 )
5X-RAY DIFFRACTION5chain 'B' and (resid 65 through 73 )
6X-RAY DIFFRACTION6chain 'B' and (resid 74 through 78 )
7X-RAY DIFFRACTION7chain 'B' and (resid 79 through 86 )
8X-RAY DIFFRACTION8chain 'B' and (resid 87 through 103 )
9X-RAY DIFFRACTION9chain 'B' and (resid 104 through 112 )
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 120 )

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