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- PDB-8x2p: The Crystal Structure of LCK from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x2p
TitleThe Crystal Structure of LCK from Biortus.
ComponentsTyrosine-protein kinase Lck
KeywordsTRANSFERASE / Kinase / Host-virus interaction / ATP-binding
Function / homology
Function and homology information


regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / Regulation of KIT signaling / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / phospholipase activator activity / leukocyte migration / CD8 receptor binding / positive regulation of T cell receptor signaling pathway / pericentriolar material / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / RHOH GTPase cycle / hemopoiesis / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / T cell receptor binding / peptidyl-tyrosine autophosphorylation / release of sequestered calcium ion into cytosol / extrinsic component of cytoplasmic side of plasma membrane / GPVI-mediated activation cascade / T cell costimulation / phosphotyrosine residue binding / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / cell surface receptor protein tyrosine kinase signaling pathway / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / platelet activation / peptidyl-tyrosine phosphorylation / activation of cysteine-type endopeptidase activity involved in apoptotic process / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of T cell activation / 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 phosphatase binding / protein tyrosine kinase activity / intracellular signal transduction / response to xenobiotic stimulus / membrane raft / protein phosphorylation / signaling receptor binding / innate immune response / protein kinase binding / extracellular exosome / ATP binding / identical protein binding / plasma membrane / 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 / SH3-like 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Tyrosine-protein kinase Lck
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Lu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of LCK from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Lu, Y.
History
DepositionNov 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Lck
B: Tyrosine-protein kinase Lck
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0197
Polymers24,5152
Non-polymers5045
Water5,188288
1
A: Tyrosine-protein kinase Lck
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5494
Polymers12,2581
Non-polymers2923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area5730 Å2
MethodPISA
2
B: Tyrosine-protein kinase Lck
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4703
Polymers12,2581
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.072, 57.438, 67.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-548-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tyrosine-protein kinase Lck


Mass: 12257.631 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 293 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: (PEGsII-A10) 0.1M MgCl2, 0.1M MES pH6.5, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→43.902 Å / Num. obs: 42896 / % possible obs: 99.4 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 30.5
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 2801

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→43.902 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.894 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2015 2101 4.898 %
Rwork0.1825 40795 -
all0.183 --
obs-42896 99.356 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0 Å2
2---0.617 Å20 Å2
3---0.777 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 32 288 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131754
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171628
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.6542366
X-RAY DIFFRACTIONr_angle_other_deg1.3421.5813754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.29820.185108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15115287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3431519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
X-RAY DIFFRACTIONr_nbd_refined0.2020.2323
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.21465
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2808
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2201
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.222
X-RAY DIFFRACTIONr_nbd_other0.1970.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2450.227
X-RAY DIFFRACTIONr_mcbond_it1.3751.533835
X-RAY DIFFRACTIONr_mcbond_other1.3631.53834
X-RAY DIFFRACTIONr_mcangle_it2.3212.2871042
X-RAY DIFFRACTIONr_mcangle_other2.3222.2891043
X-RAY DIFFRACTIONr_scbond_it1.7881.875919
X-RAY DIFFRACTIONr_scbond_other1.7871.876920
X-RAY DIFFRACTIONr_scangle_it2.9612.6891316
X-RAY DIFFRACTIONr_scangle_other2.962.6891317
X-RAY DIFFRACTIONr_lrange_it5.73220.3572005
X-RAY DIFFRACTIONr_lrange_other5.58519.3621941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.3061160.2542801X-RAY DIFFRACTION92.1352
1.436-1.4760.2571280.2262923X-RAY DIFFRACTION99.3487
1.476-1.5180.2771460.2152822X-RAY DIFFRACTION100
1.518-1.5650.2291670.1862727X-RAY DIFFRACTION100
1.565-1.6160.2091380.1842693X-RAY DIFFRACTION100
1.616-1.6730.2161500.1892557X-RAY DIFFRACTION99.9631
1.673-1.7360.1891260.1772520X-RAY DIFFRACTION99.9622
1.736-1.8070.1841330.1762394X-RAY DIFFRACTION100
1.807-1.8870.1921130.1742323X-RAY DIFFRACTION100
1.887-1.9790.2091090.1832237X-RAY DIFFRACTION100
1.979-2.0860.1951060.1742112X-RAY DIFFRACTION99.9099
2.086-2.2130.183890.1712034X-RAY DIFFRACTION100
2.213-2.3650.189980.1681882X-RAY DIFFRACTION99.9495
2.365-2.5540.1791070.1691747X-RAY DIFFRACTION100
2.554-2.7970.201730.1761635X-RAY DIFFRACTION100
2.797-3.1260.215880.1831486X-RAY DIFFRACTION100
3.126-3.6080.173650.1631342X-RAY DIFFRACTION99.8581
3.608-4.4140.166780.1661115X-RAY DIFFRACTION100
4.414-6.2230.254440.213902X-RAY DIFFRACTION100
6.223-43.9020.295270.246543X-RAY DIFFRACTION99.6503

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