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

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Basic information

Entry
Database: PDB / ID: 1cwe
TitleHUMAN P56LCK TYROSINE KINASE COMPLEXED WITH PHOSPHOPEPTIDE
Components
  • P56LCK TYROSINE KINASE
  • PHOSPHOPEPTIDE ACQ-PMP-GLU-GLU-ILE-PRO
KeywordsTRANSFERASE/PEPTIDE / PHOSPHOTRANSFERASE / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / CD27 signaling pathway / regulation of regulatory T cell differentiation / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / Fc-gamma receptor signaling pathway / FLT3 signaling through SRC family kinases / protein antigen binding / Nef Mediated CD4 Down-regulation ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / CD27 signaling pathway / regulation of regulatory T cell differentiation / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / Fc-gamma receptor signaling pathway / FLT3 signaling through SRC family kinases / protein antigen binding / Nef Mediated CD4 Down-regulation / intracellular zinc ion homeostasis / Nef and signal transduction / CD4 receptor binding / 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 / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of T cell receptor signaling pathway / protein serine/threonine phosphatase activity / pericentriolar material / PECAM1 interactions / hemopoiesis / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / Co-inhibition by PD-1 / CD28 dependent PI3K/Akt signaling / peptidyl-tyrosine autophosphorylation / phospholipase binding / T cell receptor binding / phosphatidylinositol 3-kinase binding / 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 / cell surface receptor protein tyrosine kinase signaling pathway / 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 / peptidyl-tyrosine phosphorylation / Signaling by SCF-KIT / positive regulation of T cell activation / platelet activation / Constitutive Signaling by Aberrant PI3K in Cancer / DAP12 signaling / Downstream TCR signaling / cell-cell junction / 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 / positive regulation of gene expression / 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
Tyrosine-protein kinase Lck
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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: Version format compliance
Revision 1.3Aug 3, 2011Group: Structure summary
Revision 1.4Aug 17, 2011Group: Source and taxonomy
Revision 1.5Jun 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 1.6Nov 13, 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
A: P56LCK TYROSINE KINASE
B: PHOSPHOPEPTIDE ACQ-PMP-GLU-GLU-ILE-PRO
C: P56LCK TYROSINE KINASE
D: PHOSPHOPEPTIDE ACQ-PMP-GLU-GLU-ILE-PRO


Theoretical massNumber of molelcules
Total (without water)24,0334
Polymers24,0334
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.170, 41.840, 45.520
Angle α, β, γ (deg.)68.71, 82.94, 87.36
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4149, 0.4401, -0.7964), (0.5132, -0.6096, -0.6042), (-0.7514, -0.6593, 0.0271)
Vector: 17.8814, 59.7756, 64.7106)
DetailsTHE COMPLEX CRYSTALLIZES AS A DIMER IN WHICH THE TWO MOLECULES ARE RELATED BY APPROXIMATE TWO-FOLD SYMMETRY. THE TWO MOLECULES HAVE BEEN ASSIGNED CHAIN IDENTIFIERS A AND C. RESIDUES 201 TO 205 COMPRISE THE PHOSPHOPEPTIDE. THE TWO MOLECULES HAVE BEEN ASSIGNED CHAIN IDENTIFIERS B AND D.

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Components

#1: Protein P56LCK TYROSINE KINASE


Mass: 11134.396 Da / Num. of mol.: 2 / 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, EC: 2.7.1.112
#2: Protein/peptide PHOSPHOPEPTIDE ACQ-PMP-GLU-GLU-ILE-PRO


Mass: 881.863 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized using step-wise Na-Fmoc strategy
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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 P56LCK TYROSINE KINASE ...THE REGION BETWEEN RESIDUES 3 AND 100 CORRESPONDS TO THE REGION OF THE P56LCK TYROSINE KINASE BETWEEN RESIDUES 124 AND 221.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal
*PLUS
Density % sol: 50.4 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMHEPES/NaOH1drop
213.5 %(w/v)PEG80001drop
30.02 %(w/v)1dropNaN3
42 mMLck/peptide 21drop
520 mMHEPES/NaOH1reservoir
627.0 %(w/v)PEG80001reservoir
70.04 %(w/v)1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→8 Å / Num. obs: 10015 / % possible obs: 93.9 % / Observed criterion σ(I): 2
Reflection
*PLUS
Num. all: 10015 / Num. obs: 8054 / Num. measured all: 19230 / Rmerge(I) obs: 0.06

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.3→8 Å / Rfactor Rwork: 0.192 / Rfactor obs: 0.192 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 0 216 1893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.8
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: 9897
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.3 Å2

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