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- PDB-1cwd: HUMAN P56LCK TYROSINE KINASE COMPLEXED WITH PHOSPHOPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1cwd
TitleHUMAN P56LCK TYROSINE KINASE COMPLEXED WITH PHOSPHOPEPTIDE
Components
  • (PHOSPHONOMETHYL)PHENYLALANINE-CONTAINING PEPTIDE PRO-GLU-GLY-ASP-PM3-GLU-GLU-VAL-LEU
  • P56LCK TYROSINE KINASE
KeywordsPHOSPHOTRANSFERASE/TRANSFERASE INHIBITOR / PHOSPHOTRANSFERASE / COMPLEX (PHOSPHOTRANSFERASE-PEPTIDE) / PHOSPHOTRANSFERASE-TRANSFERASE INHIBITOR 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 / 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 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Lck
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsMikol, V.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: The crystal structures of the SH2 domain of p56lck complexed with two phosphopeptides suggest a gated peptide binding site.
Authors: Mikol, V. / Baumann, G. / Keller, T.H. / Manning, U. / Zurini, M.G.
History
DepositionSep 6, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: P56LCK TYROSINE KINASE
P: (PHOSPHONOMETHYL)PHENYLALANINE-CONTAINING PEPTIDE PRO-GLU-GLY-ASP-PM3-GLU-GLU-VAL-LEU


Theoretical massNumber of molelcules
Total (without water)12,2622
Polymers12,2622
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.660, 46.660, 58.298
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 P56LCK TYROSINE KINASE


Mass: 11134.396 Da / Num. of mol.: 1 / Fragment: PHOSPHOTYROSINE RECOGNITION DOMAIN SH2
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 (PHOSPHONOMETHYL)PHENYLALANINE-CONTAINING PEPTIDE PRO-GLU-GLY-ASP-PM3-GLU-GLU-VAL-LEU


Mass: 1128.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE REGION BETWEEN RESIDUES 3 AND 100 CORRESPONDS TO THE REGION OF THE P56 LCK TYROSINE KINASE ...THE REGION BETWEEN RESIDUES 3 AND 100 CORRESPONDS TO THE REGION OF THE P56 LCK TYROSINE KINASE BETWEEN RESIDUES 124 AND 224 AND HAS BEEN ASSIGNED CHAIN IDENTIFIER "L" IN THIS ENTRY. THE PHOSPHOPEPTIDE HAS CHAIN IDENTIFIER "P".

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal
*PLUS
Density % sol: 50.2 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.05 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mM1dropCH3COOH/CH3COO- Na+
210.5 %(w/v)PEG80001drop
30.02 %(w/v)1dropNaN3
42 mMLck/peptide 11drop
520 mM1reservoirCH3COOH/CH3COO- Na+
621 %(w/v)PEG80001reservoir
70.04 %(w/v)1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→8 Å / Num. obs: 5815 / % possible obs: 95.6 %
Reflection
*PLUS
Num. all: 5815 / Num. obs: 5072 / Num. measured all: 13232 / Rmerge(I) obs: 0.077

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.25→8 Å / Rfactor Rwork: 0.185 / Rfactor obs: 0.185 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 0 129 980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection obs: 5525
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.3 Å2

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