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- PDB-5hck: HUMAN HCK SH3 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 5hck
TitleHUMAN HCK SH3 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsHEMATOPOIETIC CELL KINASE
KeywordsTRANSFERASE / SH3 / PROTEIN TYROSINE KINASE / SIGNAL TRANSDUCTION
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) / lipopolysaccharide-mediated signaling pathway / transport vesicle / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / caveola / cell projection / 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 / 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 / protein phosphorylation / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / 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 / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...Tyrosine-protein kinase HCK, SH2 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase HCK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DG, SA
AuthorsHorita, D.A. / Baldisseri, D.M. / Zhang, W. / Altieri, A.S. / Smithgall, T.E. / Gmeiner, W.H. / Byrd, R.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Solution structure of the human Hck SH3 domain and identification of its ligand binding site.
Authors: Horita, D.A. / Baldisseri, D.M. / Zhang, W. / Altieri, A.S. / Smithgall, T.E. / Gmeiner, W.H. / Byrd, R.A.
History
DepositionMar 9, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMATOPOIETIC CELL KINASE


Theoretical massNumber of molelcules
Total (without water)8,2401
Polymers8,2401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50MINIMIZED AVERAGE STRUCTURE
Representative

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Components

#1: Protein HEMATOPOIETIC CELL KINASE / HCK


Mass: 8240.034 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: RESIDUES G72-E143 OF HUMAN HCK / Plasmid: PET-14B / Gene (production host): RESIDUES G72-E143 OF HUMAN HCK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS
References: UniProt: P08631, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE JRNL ARTICLE

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Sample preparation

Sample conditionspH: 6.25 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DG, SA / Software ordinal: 1
Details: PRESENTED ENSEMBLE WAS CALCULATED USING NOE/DIHEDRAL AND 1H AND 13C CHEMICAL SHIFT RESTRAINTS.
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE STRUCTURE / Conformers calculated total number: 50 / Conformers submitted total number: 1

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