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- PDB-1lkk: HUMAN P56-LCK TYROSINE KINASE SH2 DOMAIN IN COMPLEX WITH THE PHOS... -

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Basic information

Entry
Database: PDB / ID: 1lkk
TitleHUMAN P56-LCK TYROSINE KINASE SH2 DOMAIN IN COMPLEX WITH THE PHOSPHOTYROSYL PEPTIDE AC-PTYR-GLU-GLU-ILE (PYEEI PEPTIDE)
Components
  • HUMAN P56 TYROSINE KINASE
  • PHOSPHOTYROSYL PEPTIDE AC-PTYR-GLU-GLU-ILE
KeywordsCOMPLEX (TYROSINE KINASE/PEPTIDE) / COMPLEX (TYROSINE KINASE-PEPTIDE) / COMPLEX (TYROSINE KINASE-PEPTIDE) complex
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 / 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 / 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 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / Tyrosine-protein kinase Lck
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1 Å
AuthorsTong, L.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Crystal structures of the human p56lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 A and 1.8 A resolution.
Authors: Tong, L. / Warren, T.C. / King, J. / Betageri, R. / Rose, J. / Jakes, S.
History
DepositionNov 10, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 7, 2024Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref / struct_ref_seq
Item: _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code ..._struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN P56 TYROSINE KINASE
B: PHOSPHOTYROSYL PEPTIDE AC-PTYR-GLU-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6883
Polymers12,6442
Non-polymers441
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-9 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.840, 45.040, 26.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HUMAN P56 TYROSINE KINASE


Mass: 11985.371 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06239
#2: Protein/peptide PHOSPHOTYROSYL PEPTIDE AC-PTYR-GLU-GLU-ILE


Mass: 658.591 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 mg/mlSH2 domain1drop
242 mMpeptide1drop
340 mMBES1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1 Å / Num. obs: 48786 / % possible obs: 91 % / Num. measured all: 170160 / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
SHELXL-93model building
SHELXL-93refinement
SHELXL-93phasing
RefinementResolution: 1→30 Å / σ(I): -3
Details: THE REFINEMENT WAS CARRIED OUT AGAINST F**2. REFLECTIONS THAT HAVE NEGATIVE INTENSITIES ARE INCLUDED IN THE REFINEMENT. RESIDUES 170 - 176 HAVE WEAK ELECTRON DENSITY. RESIDUES LEU 122, HIS ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST F**2. REFLECTIONS THAT HAVE NEGATIVE INTENSITIES ARE INCLUDED IN THE REFINEMENT. RESIDUES 170 - 176 HAVE WEAK ELECTRON DENSITY. RESIDUES LEU 122, HIS 148, THR 177, ARG 184, AND ARG 196 HAVE WEAK SIDE CHAIN ELECTRON DENSITY. ANISOTROPIC TEMPERATURE FACTORS WERE REFINED FOR ALL NON-HYDROGEN ATOMS. HYDROGEN ATOMS FOR THE SH2 DOMAIN AND THE INHIBITOR WERE INCLUDED IN THE REFINEMENT, WITH RIDING ISOTROPIC TEMPERATURE FACTOR VALUES. HYDROGEN ATOMS ON THE WATER MOLECULES WERE NOT INCLUDED.
RfactorNum. reflection
obs0.133 48662
Refinement stepCycle: LAST / Resolution: 1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 4 175 2004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Refine LS restraints
*PLUS
Type: s_angle_deg / Dev ideal: 1.7

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