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- PDB-5mtn: Monobody Mb(Lck_1) bound to Lck-Sh2 -

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Basic information

Entry
Database: PDB / ID: 5mtn
TitleMonobody Mb(Lck_1) bound to Lck-Sh2
Components
  • Monobody Mb(Lck_1)
  • Tyrosine-protein kinase Lck
KeywordsTRANSFERASE / Src homology 2 / Monobodies / Directed evolution
Function / homology
Function and homology information


regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / CD27 signaling pathway / Fc-gamma receptor signaling pathway / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / intracellular zinc ion homeostasis / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / CD27 signaling pathway / Fc-gamma receptor signaling pathway / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / intracellular zinc ion homeostasis / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion / Co-stimulation by CD28 / Interleukin-2 signaling / CD28 dependent Vav1 pathway / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / protein serine/threonine phosphatase activity / CD8 receptor binding / pericentriolar material / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of T cell receptor signaling pathway / phospholipase binding / PECAM1 interactions / hemopoiesis / RHOH GTPase cycle / Generation of second messenger molecules / T cell differentiation / immunological synapse / Co-inhibition by PD-1 / CD28 dependent PI3K/Akt signaling / phosphatidylinositol 3-kinase binding / T cell receptor binding / peptidyl-tyrosine autophosphorylation / positive regulation of intrinsic apoptotic signaling pathway / GPVI-mediated activation cascade / T cell costimulation / release of sequestered calcium ion into cytosol / phosphotyrosine residue binding / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / T cell activation / cell surface receptor protein tyrosine kinase signaling pathway / non-membrane spanning protein tyrosine kinase activity / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / Signaling by SCF-KIT / peptidyl-tyrosine phosphorylation / platelet activation / positive regulation of T cell activation / Constitutive Signaling by Aberrant PI3K in Cancer / DAP12 signaling / Downstream TCR signaling / PIP3 activates AKT signaling / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / protein phosphatase binding / intracellular signal transduction / protein phosphorylation / membrane raft / response to xenobiotic stimulus / signaling receptor binding / protein kinase binding / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / 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. / 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
Tyrosine-protein kinase Lck
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPojer, F. / Kukenshoner, T. / Koide, S. / Hantschel, O.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies.
Authors: Kukenshoner, T. / Schmit, N.E. / Bouda, E. / Sha, F. / Pojer, F. / Koide, A. / Seeliger, M. / Koide, S. / Hantschel, O.
History
DepositionJan 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Lck
B: Monobody Mb(Lck_1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4855
Polymers23,1972
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-38 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.397, 91.397, 88.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Tyrosine-protein kinase Lck / Leukocyte C-terminal Src kinase / LSK / Lymphocyte cell-specific protein-tyrosine kinase / Protein ...Leukocyte C-terminal Src kinase / LSK / Lymphocyte cell-specific protein-tyrosine kinase / Protein YT16 / Proto-oncogene Lck / T cell-specific protein-tyrosine kinase / p56-LCK


Mass: 13142.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCK
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P06239, non-specific protein-tyrosine kinase
#2: Protein Monobody Mb(Lck_1)


Mass: 10054.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 5.32 Å3/Da / Density % sol: 76.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0,2M Lithium sulfate / 0.1M TRIS pH8.5 / 10% PEG8K + 10%PEG1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→45.7 Å / Num. obs: 10316 / % possible obs: 100 % / Redundancy: 5.5 % / Net I/σ(I): 23.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→45.7 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.606 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.295 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26503 544 5.3 %RANDOM
Rwork0.22751 ---
obs0.22944 10316 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.567 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.85→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 15 0 1439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191476
X-RAY DIFFRACTIONr_bond_other_d0.0020.021346
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9612012
X-RAY DIFFRACTIONr_angle_other_deg0.93833106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31722.74262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.28315221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.515159
X-RAY DIFFRACTIONr_chiral_restr0.0680.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211633
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02342
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_it2.7957.822725
X-RAY DIFFRACTIONr_mcbond_other2.7957.82724
X-RAY DIFFRACTIONr_mcangle_it4.70311.714901
X-RAY DIFFRACTIONr_mcangle_other4.70111.717902
X-RAY DIFFRACTIONr_scbond_it2.6448.101751
X-RAY DIFFRACTIONr_scbond_other2.5998.047740
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.30711.9671094
X-RAY DIFFRACTIONr_long_range_B_refined7.24762.2591551
X-RAY DIFFRACTIONr_long_range_B_other7.24562.2821552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.853→2.927 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 46 -
Rwork0.375 693 -
obs--99.46 %

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