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- PDB-6c4s: Human cSrc SH3 Domain in complex with Choline Kinase fragment 60-69 -

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Basic information

Entry
Database: PDB / ID: 6c4s
TitleHuman cSrc SH3 Domain in complex with Choline Kinase fragment 60-69
ComponentsProto-oncogene tyrosine-protein kinase Src,cSrc SH3 Domain
KeywordsTRANSFERASE / PEPTIDE BINDING PROTEIN / enzyme / non-receptor tyrosine kinase
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of integrin activation ...regulation of caveolin-mediated endocytosis / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of integrin activation / BMP receptor binding / negative regulation of focal adhesion assembly / Activated NTRK2 signals through FYN / intestinal epithelial cell development / focal adhesion assembly / Netrin mediated repulsion signals / negative regulation of neutrophil activation / bone resorption / positive regulation of small GTPase mediated signal transduction / connexin binding / Activated NTRK3 signals through PI3K / signal complex assembly / regulation of vascular permeability / Co-stimulation by CD28 / EPH-Ephrin signaling / podosome / positive regulation of lamellipodium morphogenesis / DCC mediated attractive signaling / regulation of bone resorption / Regulation of RUNX1 Expression and Activity / stress fiber assembly / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / leukocyte migration / MET activates PTK2 signaling / Regulation of KIT signaling / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / Signaling by ALK / phospholipase activator activity / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / positive regulation of Rac protein signal transduction / stimulatory C-type lectin receptor signaling pathway / Receptor Mediated Mitophagy / Signaling by EGFR / negative regulation of intrinsic apoptotic signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / regulation of cell-cell adhesion / GRB2:SOS provides linkage to MAPK signaling for Integrins / progesterone receptor signaling pathway / RHOU GTPase cycle / Recycling pathway of L1 / positive regulation of epithelial cell migration / RET signaling / regulation of heart rate by cardiac conduction / FCGR activation / signaling receptor activator activity / negative regulation of anoikis / Long-term potentiation / EPH-ephrin mediated repulsion of cells / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / transforming growth factor beta receptor signaling pathway / GAB1 signalosome / negative regulation of hippo signaling / protein tyrosine kinase activator activity / T cell costimulation / Nuclear signaling by ERBB4 / lactation / osteoclast differentiation / negative regulation of protein-containing complex assembly / ephrin receptor binding / phospholipase binding / Signaling by ERBB2 / Integrin signaling / p38MAPK events / EPHB-mediated forward signaling / positive regulation of TORC1 signaling / peptidyl-tyrosine phosphorylation / NCAM signaling for neurite out-growth / Downstream signal transduction / FCGR3A-mediated IL10 synthesis / ionotropic glutamate receptor binding / positive regulation of glycolytic process / SH2 domain binding / integrin-mediated signaling pathway / response to interleukin-1 / negative regulation of extrinsic apoptotic signaling pathway / Downregulation of ERBB4 signaling / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / InlA-mediated entry of Listeria monocytogenes into host cells / angiotensin-activated signaling pathway
Similarity search - Function
SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / 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 / 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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsKall, S.L. / Lavie, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5T32DE018381-10 United States
CitationJournal: Sci Rep / Year: 2019
Title: Molecular basis for the interaction between human choline kinase alpha and the SH3 domain of the c-Src tyrosine kinase.
Authors: Kall, S.L. / Whitlatch, K. / Smithgall, T.E. / Lavie, A.
History
DepositionJan 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src,cSrc SH3 Domain
B: Proto-oncogene tyrosine-protein kinase Src,cSrc SH3 Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4674
Polymers16,3362
Non-polymers1312
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Dimer is crystallographic in nature
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-49 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.117, 38.753, 57.966
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src,cSrc SH3 Domain / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 8168.078 Da / Num. of mol.: 2 / Fragment: SH3 domain residues 87-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Production host: Escherichia coli (E. coli)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Zinc Acetate 0.1 M Sodium Cacodylate pH 6.5 10% v/v Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→57.68 Å / Num. obs: 39617 / % possible obs: 90.2 % / Redundancy: 1.67 % / Net I/σ(I): 7.45
Reflection shellResolution: 1.5→1.59 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOLREPphasing
RefinementResolution: 1.5→57.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.511 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22626 1046 4.9 %RANDOM
Rwork0.18717 ---
obs0.18912 20257 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.734 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å2-0.85 Å2
2--0.03 Å20 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 1.5→57.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 2 141 1299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021194
X-RAY DIFFRACTIONr_bond_other_d0.0020.021052
X-RAY DIFFRACTIONr_angle_refined_deg1.951.981639
X-RAY DIFFRACTIONr_angle_other_deg1.07632462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01224.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81515172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.323154
X-RAY DIFFRACTIONr_chiral_restr0.110.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211322
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02230
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5942.362590
X-RAY DIFFRACTIONr_mcbond_other2.5822.36589
X-RAY DIFFRACTIONr_mcangle_it4.0443.524734
X-RAY DIFFRACTIONr_mcangle_other4.0433.527735
X-RAY DIFFRACTIONr_scbond_it3.252.627604
X-RAY DIFFRACTIONr_scbond_other3.2472.628604
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8833.84905
X-RAY DIFFRACTIONr_long_range_B_refined7.52829.0041353
X-RAY DIFFRACTIONr_long_range_B_other7.4428.4481319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 59 -
Rwork0.307 1479 -
obs--95.06 %

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