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- PDB-1qcf: CRYSTAL STRUCTURE OF HCK IN COMPLEX WITH A SRC FAMILY-SELECTIVE T... -

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Basic information

Entry
Database: PDB / ID: 1qcf
TitleCRYSTAL STRUCTURE OF HCK IN COMPLEX WITH A SRC FAMILY-SELECTIVE TYROSINE KINASE INHIBITOR
ComponentsTyrosine-protein kinase HCK
KeywordsTYROSINE KINASE / TYROSINE KINASE-INHIBITOR COMPLEX / DOWN-REGULATED KINASE / ORDERED ACTIVATION LOOP
Function / homology
Function and homology information


leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / localization / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / transport vesicle / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / cell projection / caveola / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / regulation of inflammatory response / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / lysosome / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / signaling receptor binding / protein phosphorylation / focal adhesion / innate immune response / intracellular membrane-bounded organelle / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase HCK, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains ...Tyrosine-protein kinase HCK, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / 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 / Roll / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-PP1 / Tyrosine-protein kinase HCK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsSchindler, T. / Sicheri, F. / Pico, A. / Gazit, A. / Levitzki, A. / Kuriyan, J.
CitationJournal: Mol.Cell / Year: 1999
Title: Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor.
Authors: Schindler, T. / Sicheri, F. / Pico, A. / Gazit, A. / Levitzki, A. / Kuriyan, J.
History
DepositionMay 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _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 HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2822
Polymers52,0001
Non-polymers2811
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.015, 99.002, 103.387
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase HCK / Hematopoietic cell kinase / Hemopoietic cell kinase / p59-HCK/p60-HCK / p59Hck / p61Hck


Mass: 52000.227 Da / Num. of mol.: 1 / Fragment: SH3-SH2-KINASE-HIGH AFFINITY TAIL / Mutation: Q528E, Q529E, Q530I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCK
References: UniProt: P08631, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PP1 / 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE


Mass: 281.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 10000, DIMETHYL SULFOXIDE, N-(2-HYDROXYETHYL)PIPERAZINE-N-(2- ETHANESULFONIC ACID), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mMprotein1drop
220 %DMSO1drop
328 %(w/v)PEG100001reservoir
4100 mMHEPES/NaOH1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 35649 / Num. obs: 35042 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 28.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.277 / % possible all: 95.2
Reflection
*PLUS
Num. measured all: 426133
Reflection shell
*PLUS
% possible obs: 95.2 % / Num. unique obs: 4250 / Num. measured obs: 23990

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2→99 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.257 3475 -
Rwork0.215 --
all-35649 -
obs-35005 98.1 %
Refinement stepCycle: LAST / Resolution: 2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 21 312 3959
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007258
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.54111
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.54

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