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- PDB-2hck: SRC FAMILY KINASE HCK-QUERCETIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2hck
TitleSRC FAMILY KINASE HCK-QUERCETIN COMPLEX
ComponentsHEMATOPOETIC CELL KINASE HCK
KeywordsTRANSFERASE / PROTEIN TYROSINE KINASE / SIGNAL TRANSDUCTION / SH2 / SH3
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
PRD domain protein, EF0829/AHA3910 / PRD domain / PRD domain superfamily / PRD domain profile. / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / SH3 type barrels. ...PRD domain protein, EF0829/AHA3910 / PRD domain / PRD domain superfamily / PRD domain profile. / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / SH3 type barrels. / Protein tyrosine and serine/threonine kinase / Roll / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3,5,7,3',4'-PENTAHYDROXYFLAVONE / PRD domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS/MAD / Resolution: 3 Å
AuthorsSicheri, F. / Moarefi, I. / Kuriyan, J.
CitationJournal: Nature / Year: 1997
Title: Crystal structure of the Src family tyrosine kinase Hck.
Authors: Sicheri, F. / Moarefi, I. / Kuriyan, J.
History
DepositionFeb 25, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMATOPOETIC CELL KINASE HCK
B: HEMATOPOETIC CELL KINASE HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2936
Polymers100,6092
Non-polymers6854
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.500, 93.300, 176.900
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 HEMATOPOETIC CELL KINASE HCK


Mass: 50304.348 Da / Num. of mol.: 2 / Fragment: SH3-SH2-KINASE-REGULATORY TAIL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Gene: HUMAN HCK / Cell line (production host): SF9 / Gene (production host): HUMAN HCK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08631, EC: 2.7.1.112
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE ORIENTATION PLANES OF THE QUERCETIN INHIBITORS IN BOTH HCK MOLECULES OF THE ASYMMETRIC UNIT ARE ...THE ORIENTATION PLANES OF THE QUERCETIN INHIBITORS IN BOTH HCK MOLECULES OF THE ASYMMETRIC UNIT ARE RELIABLY DETERMINED. THE POSITION AND ORIENTATION OF THE QUERCETIN INHIBITOR IN HCK MOLECULE 1 AND THE POSITION OF THE BRIDGING WATER MOLECULE, HOH 4, IS RELIABLY DETERMINED AS CONFIRMED BY 'SIMULATED ANNEALING OMIT' ELECTRON DENSITY MAPS. THE ORIENTATION AND POSITION OF THE QUERCETIN INHIBITOR IN HCK MOLECULE 2 IS NOT RELIABLY DETERMINED. BOOMERANG SHAPED PLANAR ELECTRON DENSITY CAN BE EQUALLY ACCOUNTED FOR BY TWO ORIENTATIONS OF THE QUERCETIN INHIBITOR. THE TWO ORIENTATIONS ARE RELATED BY A 180 DEGREE ROTATION PERPENDICULAR TO THE LONG AXIS OF THE QUERCETIN MOLECULE. THE AUTHORS HAVE CHOSEN TO MODEL THE QUERCETIN INHIBITOR IN HCK MOLECULE 2 IN THE SAME ORIENTATION AS THAT RELIABLY DETERMINED FOR THE QUERCETIN INHIBITOR IN HCK MOLECULE 1.

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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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 292 K / pH: 6.5
Details: HANGING DROPS (1UL) OF 50MG/ML PROTEIN AND 10MM QUERCETIN WERE MIXED WITH EQUAL VOLUMES OF RESERVOIR BUFFER CONTAINING 150 MM CALCIUM ACETATE, 100MM CACODYLATE (PH 6.5), 7% PEG 8000 AND 16% ...Details: HANGING DROPS (1UL) OF 50MG/ML PROTEIN AND 10MM QUERCETIN WERE MIXED WITH EQUAL VOLUMES OF RESERVOIR BUFFER CONTAINING 150 MM CALCIUM ACETATE, 100MM CACODYLATE (PH 6.5), 7% PEG 8000 AND 16% V/V ETHYLENE GLYCOL. THE MIXED DROPS WERE THEN SEEDED AND STORED AT 19 DEGREES C., temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mg/mlprotein1drop
210 mMquercetin1dropor 2AMP-PMP
3150 mMcalcium acetate1reservoir
4100 mMcacodylate 1reservoir
57 %(w/v)PEG80001reservoir
616 %(v/v)ehthylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→18 Å / Num. obs: 385451 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 15.7 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 17.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.145 / % possible all: 96.4
Reflection
*PLUS
Num. obs: 24477 / Num. measured all: 385451
Reflection shell
*PLUS
% possible obs: 96.4 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIRAS/MAD / Resolution: 3→18 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.311 1224 5 %RANDOM
Rwork0.228 ---
obs0.228 24477 98.1 %-
Displacement parametersBiso mean: 57.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2---18.3 Å20 Å2
3---17.4 Å2
Refinement stepCycle: LAST / Resolution: 3→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 46 2 7020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.9
X-RAY DIFFRACTIONx_mcangle_it3.4
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.423 58 5 %
Rwork0.355 1655 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.355

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