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- PDB-5dc9: CRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL B -

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Basic information

Entry
Database: PDB / ID: 5dc9
TitleCRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL B
Components
  • AS25 monobody
  • Tyrosine-protein kinase ABL1
KeywordsPROTEIN BINDING / ENGINEERED BINDING PROTEIN / ANTIBODY MIMIC / PROTEIN-PROTEIN COMPLEX / SH2 DOMAIN / TYROSINE-PROTEIN KINASE
Function / homology
Function and homology information


negative regulation of monocyte activation / : / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / negative regulation of transforming growth factor beta production / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / Extracellular matrix organization / response to epinephrine ...negative regulation of monocyte activation / : / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / negative regulation of transforming growth factor beta production / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / Extracellular matrix organization / response to epinephrine / activation of protein kinase C activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / transitional one stage B cell differentiation / calcium-independent cell-matrix adhesion / Fibronectin matrix formation / regulation of postsynaptic specialization assembly / neural crest cell migration involved in autonomic nervous system development / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / cerebellum morphogenesis / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of extracellular matrix organization / fibrinogen complex / microspike assembly / B-1 B cell homeostasis / peptide cross-linking / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / regulation of cell motility / mitochondrial depolarization / integrin activation / ALK mutants bind TKIs / positive regulation of establishment of T cell polarity / activated T cell proliferation / cellular response to dopamine / positive regulation of blood vessel branching / cell-substrate junction assembly / proline-rich region binding / negative regulation of mitotic cell cycle / regulation of protein phosphorylation / regulation of Cdc42 protein signal transduction / proteoglycan binding / syntaxin binding / mitogen-activated protein kinase binding / regulation of hematopoietic stem cell differentiation / alpha-beta T cell differentiation / positive regulation of dendrite development / positive regulation of cell migration involved in sprouting angiogenesis / extracellular matrix structural constituent / peptidyl-tyrosine autophosphorylation / biological process involved in interaction with symbiont / regulation of axon extension / positive regulation of peptidyl-tyrosine phosphorylation / Molecules associated with elastic fibres / regulation of T cell differentiation / MET activates PTK2 signaling / peptidase activator activity / negative regulation of cell-cell adhesion / HDR through Single Strand Annealing (SSA) / neuromuscular process controlling balance / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / positive regulation of osteoblast proliferation / Myogenesis / response to muscle activity / positive regulation of vasoconstriction / platelet-derived growth factor receptor-beta signaling pathway / RUNX2 regulates osteoblast differentiation / endoplasmic reticulum-Golgi intermediate compartment / Fc-gamma receptor signaling pathway involved in phagocytosis / endodermal cell differentiation / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / Bergmann glial cell differentiation / regulation of microtubule polymerization / myoblast proliferation / associative learning / negative regulation of long-term synaptic potentiation / negative regulation of cellular senescence / basement membrane / Non-integrin membrane-ECM interactions / actin monomer binding / negative regulation of BMP signaling pathway / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / RHO GTPases Activate WASPs and WAVEs / canonical NF-kappaB signal transduction / cardiac muscle cell proliferation / ECM proteoglycans / BMP signaling pathway / ephrin receptor signaling pathway / Integrin cell surface interactions
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / SH2 domain / SHC Adaptor Protein / : / Kringle-like fold / Fibronectin type III domain / EGF-like domain signature 1. / SH3 domain / Fibronectin type 3 domain / SH2 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Tyrosine-protein kinase ABL1 / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.56 Å
AuthorsWojcik, J.B. / Koide, A. / Koide, S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface.
Authors: Wojcik, J. / Lamontanara, A.J. / Grabe, G. / Koide, A. / Akin, L. / Gerig, B. / Hantschel, O. / Koide, S.
History
DepositionAug 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Data collection
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: AS25 monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5959
Polymers23,9962
Non-polymers5997
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-8 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.391, 66.391, 112.797
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 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: 13715.132 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Protein AS25 monobody


Mass: 10281.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02751*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Imidazole pH 8.5 and 3.4M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2012
RadiationMonochromator: SI 111 SIDE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.56→57.22 Å / Num. obs: 36108 / % possible obs: 98.2 % / Redundancy: 8.5 % / Rsym value: 0.055 / Net I/σ(I): 34.4
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.3 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data collection
RefinementResolution: 1.56→57.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.911 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1706 1803 5 %RANDOM
Rwork0.13652 ---
obs0.13823 34131 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20 Å2
2--0.21 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.56→57.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 40 232 1790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021641
X-RAY DIFFRACTIONr_bond_other_d00.021099
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9652238
X-RAY DIFFRACTIONr_angle_other_deg0.81832670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.04922.568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.29815242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1341510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr17.43932740
X-RAY DIFFRACTIONr_sphericity_free22.432578
X-RAY DIFFRACTIONr_sphericity_bonded15.04352850
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 114 -
Rwork0.205 2198 -
obs--93.11 %

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