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- PDB-3lck: THE KINASE DOMAIN OF HUMAN LYMPHOCYTE KINASE (LCK), ACTIVATED FOR... -

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Basic information

Entry
Database: PDB / ID: 3lck
TitleTHE KINASE DOMAIN OF HUMAN LYMPHOCYTE KINASE (LCK), ACTIVATED FORM (AUTO-PHOSPHORYLATED ON TYR394)
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE
KeywordsTYROSINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / SIGNAL TRANSDUCTION
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 / CD4 receptor binding / positive regulation of heterotypic cell-cell adhesion / Nef and signal transduction / Co-stimulation by CD28 / Interleukin-2 signaling / CD28 dependent Vav1 pathway / peptidyl-tyrosine autophosphorylation / 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 / pericentriolar material / protein serine/threonine phosphatase activity / PECAM1 interactions / hemopoiesis / Generation of second messenger molecules / RHOH GTPase cycle / T cell differentiation / immunological synapse / Co-inhibition by PD-1 / CD28 dependent PI3K/Akt signaling / T cell receptor binding / phosphatidylinositol 3-kinase binding / phospholipase 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 / peptidyl-tyrosine phosphorylation / 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 / positive regulation of T cell activation / platelet activation / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell junction / Downstream TCR signaling / DAP12 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 / protein phosphorylation / intracellular signal transduction / 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 / cytoplasm / cytosol
Similarity search - Function
Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / : / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Lck
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MOLECULAR REPLACEMENT, MAD / Resolution: 1.7 Å
AuthorsYamaguchi, H. / Hendrickson, W.A.
CitationJournal: Nature / Year: 1996
Title: Structural basis for activation of human lymphocyte kinase Lck upon tyrosine phosphorylation.
Authors: Yamaguchi, H. / Hendrickson, W.A.
History
DepositionApr 8, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5222
Polymers31,4261
Non-polymers961
Water6,125340
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.040, 73.620, 91.170
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 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE / LCK


Mass: 31425.865 Da / Num. of mol.: 1 / Fragment: PROTEIN TYROSINE KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATION ON TYR 394 / Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Gene: LCK / Plasmid: PFASTBAC-1-BMON14272 / Cell line (production host): SF9 / Cellular location (production host): CYTOPLASM / Gene (production host): POLYHEDRIN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06239, EC: 2.7.1.112
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PROTEIN WAS CRYSTALLIZED IN HANGING DROPS WITH 1.6 M AMMONIUM SULFATE AND 0.1 M BISTRIS-HCL (PH 6.5 @ RT) AS A WELL SOLUTION., vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.51 mg/mlprotein1drop
20.080 mMATP1drop
30.080 mMsubstrate peptide1drop
40.6 Mammonium sulfate1drop
50.05 MBis-Tris1drop
61.6 Mammonium sulfate1reservoir
70.1 Mbis-Tris1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jul 21, 1996 / Details: SAGITTAL FOCUSING MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 31599 / % possible obs: 99 % / Redundancy: 8.1 % / Biso Wilson estimate: 13 Å2 / Rsym value: 0.028 / Net I/σ(I): 37
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 21.8 / Rsym value: 0.047 / % possible all: 96.1
Reflection
*PLUS
Rmerge(I) obs: 0.028
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.047

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Processing

Software
NameVersionClassification
MADSYSphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT, MAD
Starting model: PDB ENTRY 1IRK

1irk


Resolution: 1.7→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED
Cross valid method: R FREE THROUGHOUT EXCEPT FOR THE LAST ROUND
σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.199 -10 %RANDOM
Rwork0.178 ---
obs0.178 31241 98.95 %-
Displacement parametersBiso mean: 10.37 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 5 340 2692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.86
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.448
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
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.226 -10 %
Rwork0.209 3876 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.86
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.448

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