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- PDB-5mtm: Monobody Mb(Lck_3) bound to Lck-SH2 domain -

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Basic information

Entry
Database: PDB / ID: 5mtm
TitleMonobody Mb(Lck_3) bound to Lck-SH2 domain
Components
  • Monobody Mb(Lck_3)
  • Tyrosine-protein kinase Lck
KeywordsTRANSFERASE / Src homology domain / Monobodies
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 / Co-stimulation by CD28 / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / intracellular zinc ion homeostasis / Nef and signal transduction ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / CD27 signaling pathway / Fc-gamma receptor signaling pathway / Co-stimulation by CD28 / 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 / 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 / positive regulation of T cell receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / phospholipase binding / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / hemopoiesis / Generation of second messenger molecules / T cell differentiation / RHOH GTPase cycle / immunological synapse / Co-inhibition by PD-1 / phosphatidylinositol 3-kinase binding / T cell receptor binding / peptidyl-tyrosine autophosphorylation / positive regulation of intrinsic apoptotic signaling pathway / GPVI-mediated activation cascade / release of sequestered calcium ion into cytosol / T cell costimulation / phosphotyrosine residue binding / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / : / T cell activation / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / Signaling by SCF-KIT / peptidyl-tyrosine phosphorylation / platelet activation / positive regulation of T cell activation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / Downstream TCR signaling / PIP3 activates AKT signaling / DAP12 signaling / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / protein phosphatase binding / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / intracellular signal transduction / protein phosphorylation / membrane raft / response to xenobiotic stimulus / signaling receptor binding / innate immune response / 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 / 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. / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.405 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 1.2Mar 7, 2018Group: Source and taxonomy / Structure summary / Category: entity / entity_src_nat / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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_3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4114
Polymers23,2802
Non-polymers1312
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-43 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.834, 81.834, 105.961
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 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 (E. coli)
References: UniProt: P06239, non-specific protein-tyrosine kinase
#2: Protein Monobody Mb(Lck_3)


Mass: 10137.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH6.5, 15 % PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40.92 Å / Num. obs: 14544 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 37.91

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.405→40.917 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 28.23
RfactorNum. reflection% reflection
Rfree0.2568 1335 5.01 %
Rwork0.2054 --
obs0.2078 14544 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.405→40.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 2 32 1584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121598
X-RAY DIFFRACTIONf_angle_d1.1592183
X-RAY DIFFRACTIONf_dihedral_angle_d13.157934
X-RAY DIFFRACTIONf_chiral_restr0.062242
X-RAY DIFFRACTIONf_plane_restr0.008283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4046-2.49050.38261300.3082497X-RAY DIFFRACTION99
2.4905-2.59020.3191330.27492529X-RAY DIFFRACTION100
2.5902-2.70810.31451310.2622557X-RAY DIFFRACTION100
2.7081-2.85080.28421350.25052523X-RAY DIFFRACTION100
2.8508-3.02940.27471350.23022543X-RAY DIFFRACTION100
3.0294-3.26320.36531320.23162540X-RAY DIFFRACTION100
3.2632-3.59140.24241340.21772541X-RAY DIFFRACTION100
3.5914-4.11070.26831330.20652541X-RAY DIFFRACTION100
4.1107-5.17740.20411330.16392533X-RAY DIFFRACTION100
5.1774-40.92290.24171390.19122521X-RAY DIFFRACTION100

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