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- PDB-3mss: Abl kinase in complex with imatinib and fragment (FRAG2) in the m... -

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Basic information

Entry
Database: PDB / ID: 3mss
TitleAbl kinase in complex with imatinib and fragment (FRAG2) in the myristate site
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / fragment-based screening / FBS / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process ...Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to epinephrine / regulation of cellular senescence / regulation of modification of synaptic structure / positive regulation of extracellular matrix organization / delta-catenin binding / B cell proliferation involved in immune response / Regulation of actin dynamics for phagocytic cup formation / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / Myogenesis / regulation of Cdc42 protein signal transduction / activated T cell proliferation / regulation of axon extension / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / syntaxin binding / cardiac muscle cell proliferation / regulation of T cell differentiation / negative regulation of double-strand break repair via homologous recombination / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / regulation of microtubule polymerization / B cell proliferation / positive regulation of osteoblast proliferation / cell leading edge / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / Bergmann glial cell differentiation / associative learning / neuromuscular process controlling balance / platelet-derived growth factor receptor signaling pathway / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / endothelial cell migration / positive regulation of T cell migration / canonical NF-kappaB signal transduction / BMP signaling pathway / phagocytosis / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / signal transduction in response to DNA damage / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / actin filament polymerization / SH2 domain binding / response to endoplasmic reticulum stress / phosphotyrosine residue binding / ephrin receptor binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / post-embryonic development / protein kinase C binding / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of endothelial cell migration / thymus development / neural tube closure / integrin-mediated signaling pathway / establishment of localization in cell / regulation of actin cytoskeleton organization / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / neuron differentiation / cellular response to hydrogen peroxide / autophagy
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 / Src homology 3 domains ...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
O-benzyl-N-methyl-L-tyrosinamide / Chem-STI / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCowan-Jacob, S.W. / Rummel, G. / Fendrich, G.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Binding or bending: distinction of allosteric Abl kinase agonists from antagonists by an NMR-based conformational assay.
Authors: Jahnke, W. / Grotzfeld, R.M. / Pelle, X. / Strauss, A. / Fendrich, G. / Cowan-Jacob, S.W. / Cotesta, S. / Fabbro, D. / Furet, P. / Mestan, J. / Marzinzik, A.L.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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
C: Tyrosine-protein kinase ABL1
D: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,08612
Polymers134,9744
Non-polymers3,1128
Water13,097727
1
A: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5213
Polymers33,7441
Non-polymers7782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5213
Polymers33,7441
Non-polymers7782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5213
Polymers33,7441
Non-polymers7782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5213
Polymers33,7441
Non-polymers7782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.219, 146.780, 95.812
Angle α, β, γ (deg.)90.00, 127.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-627-

HOH

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Components

#1: Protein
Tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Proto-oncogene c-Abl / p150


Mass: 33743.523 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN, residues 229-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00520, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-STI / 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE / STI-571 / IMATINIB / Imatinib


Mass: 493.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H31N7O / Comment: medication, inhibitor*YM
#3: Chemical
ChemComp-MS7 / O-benzyl-N-methyl-L-tyrosinamide


Mass: 284.353 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H20N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: Buffer: 0.1M imidazole pH 6.5, 0.2M MgCl2, 2%EG, 13.8% PEG4000, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→52.93 Å / Num. all: 89303 / Num. obs: 89303 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.25 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.3
Reflection shellResolution: 1.95→2.04 Å / Redundancy: 1.98 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.85 / Num. unique all: 9031 / % possible all: 78.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IEP.PDB

1iep


Resolution: 1.95→52.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.481 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 4461 5 %RANDOM
Rwork0.16949 ---
obs0.17203 84760 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.453 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0.83 Å2
2---0.42 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.95→52.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8604 0 232 727 9563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229076
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.98412264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57451040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22123.981412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.672151548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1391544
X-RAY DIFFRACTIONr_chiral_restr0.1470.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216876
X-RAY DIFFRACTIONr_mcbond_it1.2541.55252
X-RAY DIFFRACTIONr_mcangle_it2.21628456
X-RAY DIFFRACTIONr_scbond_it3.49333824
X-RAY DIFFRACTIONr_scangle_it5.4244.53808
LS refinement shellResolution: 1.955→2.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 254 -
Rwork0.268 4842 -
obs--74.68 %
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)
10.52640.12420.04290.97930.24071.21190.0422-0.06390.06730.0441-0.0285-0.086-0.0936-0.09-0.01370.0680.01680.01120.0363-0.02820.052112.028-0.161-22.458
20.551-0.10950.09351.4764-0.3570.74550.0821-0.0341-0.03380.1096-0.0558-0.01440.01250.0431-0.02620.072-0.0319-0.00090.06690.02580.019840.89-35.296-19.426
30.51470.11410.04471.0304-0.30951.15720.0381-0.0649-0.07590.0461-0.02660.09430.07560.0857-0.01150.06350.0220.00710.03620.0320.0531-12.263-37.823-22.441
40.5731-0.0674-0.08421.51190.33490.73430.0781-0.03190.03790.1301-0.05250.0219-0.0067-0.0398-0.02550.0726-0.03590.01130.0609-0.0250.01616.963-76.079-19.408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A225 - 498
2X-RAY DIFFRACTION1A1
3X-RAY DIFFRACTION2B225 - 498
4X-RAY DIFFRACTION2B1
5X-RAY DIFFRACTION3C225 - 498
6X-RAY DIFFRACTION3C1
7X-RAY DIFFRACTION4D225 - 498
8X-RAY DIFFRACTION4D1

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