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- PDB-2zv8: Lyn Tyrosine Kinase Domain-AMP-PNP complex -

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Basic information

Entry
Database: PDB / ID: 2zv8
TitleLyn Tyrosine Kinase Domain-AMP-PNP complex
ComponentsTyrosine-protein kinase Lyn
KeywordsTRANSFERASE / Lyn Kinase AMPPNP / Alternative splicing / ATP-binding / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Palmitate / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


Growth hormone receptor signaling / negative regulation of myeloid leukocyte differentiation / erythropoietin receptor binding / C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / Signaling by Erythropoietin / response to sterol depletion / regulation of mast cell activation / Platelet Adhesion to exposed collagen / Fc epsilon receptor (FCERI) signaling ...Growth hormone receptor signaling / negative regulation of myeloid leukocyte differentiation / erythropoietin receptor binding / C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / Signaling by Erythropoietin / response to sterol depletion / regulation of mast cell activation / Platelet Adhesion to exposed collagen / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / PECAM1 interactions / CD22 mediated BCR regulation / negative regulation of intracellular signal transduction / positive regulation of oligodendrocyte progenitor proliferation / Signaling by CSF3 (G-CSF) / Erythropoietin activates RAS / eosinophil differentiation / Regulation of KIT signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / Co-stimulation by CD28 / Fc receptor mediated inhibitory signaling pathway / EPH-ephrin mediated repulsion of cells / GPVI-mediated activation cascade / regulation of B cell receptor signaling pathway / EPHB-mediated forward signaling / FCERI mediated MAPK activation / Inactivation of CSF3 (G-CSF) signaling / negative regulation of toll-like receptor 2 signaling pathway / Signaling by SCF-KIT / tolerance induction to self antigen / FCGR activation / integrin alpha2-beta1 complex / Cyclin D associated events in G1 / positive regulation of mast cell proliferation / negative regulation of mast cell proliferation / glycosphingolipid binding / immune response-regulating cell surface receptor signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemoglobin biosynthetic process / FCERI mediated Ca+2 mobilization / platelet degranulation / regulation of mast cell degranulation / negative regulation of toll-like receptor 4 signaling pathway / FCERI mediated NF-kB activation / Cell surface interactions at the vascular wall / Regulation of signaling by CBL / regulation of platelet aggregation / phosphorylation-dependent protein binding / dendritic cell differentiation / regulation of B cell apoptotic process / neuroinflammatory response / CD209 (DC-SIGN) signaling / phosphatidylinositol 3-kinase activator activity / interleukin-5-mediated signaling pathway / oligodendrocyte development / histamine secretion by mast cell / regulation of release of sequestered calcium ion into cytosol / gamma-tubulin binding / response to carbohydrate / platelet-derived growth factor receptor binding / toll-like receptor 4 signaling pathway / postsynaptic specialization, intracellular component / negative regulation of B cell proliferation / mitochondrial crista / regulation of cell adhesion mediated by integrin / hemopoiesis / B cell homeostasis / negative regulation of protein phosphorylation / negative regulation of MAP kinase activity / response to amino acid / response to axon injury / fatty acid transport / hematopoietic progenitor cell differentiation / regulation of ERK1 and ERK2 cascade / positive regulation of phosphorylation / cellular response to retinoic acid / positive regulation of glial cell proliferation / response to hormone / ephrin receptor binding / regulation of cytokine production / lipopolysaccharide-mediated signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / erythrocyte differentiation / DNA damage checkpoint signaling / adherens junction / non-membrane spanning protein tyrosine kinase activity / B cell receptor signaling pathway / phosphoprotein binding / response to insulin / non-specific protein-tyrosine kinase / regulation of erythrocyte differentiation / : / negative regulation of ERK1 and ERK2 cascade / cell morphogenesis
Similarity search - Function
Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains ...Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / : / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Tyrosine-protein kinase Lyn
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWilliams, N.K. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structures of the Lyn Protein Tyrosine Kinase Domain in Its Apo- and Inhibitor-bound State
Authors: Williams, N.K. / Lucet, I.S. / Klinken, S.P. / Ingley, E. / Rossjohn, J.
History
DepositionNov 4, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Lyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3172
Polymers31,8111
Non-polymers5061
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.239, 127.239, 54.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Tyrosine-protein kinase Lyn


Mass: 31810.639 Da / Num. of mol.: 1 / Fragment: Kinase Domain, residues 239-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P25911, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 1 IN THE DATABASE, LYN_MOUSE.

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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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23% polyethylene glycol 3350, 0.1M NaCl, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→38.9 Å / Num. obs: 9082

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QPD

1qpd


Resolution: 2.7→36.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 27.54 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 1.563 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24493 417 4.6 %RANDOM
Rwork0.19916 ---
obs0.20134 8665 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.943 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 31 15 2090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222134
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.992891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98424.02387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09115376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8681510
X-RAY DIFFRACTIONr_chiral_restr0.0720.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021567
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2987
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21438
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.81531325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5152073
X-RAY DIFFRACTIONr_scbond_it2.3327948
X-RAY DIFFRACTIONr_scangle_it3.410818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 30 -
Rwork0.337 641 -
obs--100 %

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