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- PDB-6f3f: Autoinhibited Src kinase bound to ADP -

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Basic information

Entry
Database: PDB / ID: 6f3f
TitleAutoinhibited Src kinase bound to ADP
ComponentsTyrosine-protein kinase
KeywordsSIGNALING PROTEIN / kinase / ADP / autoinhibited
Function / homology
Function and homology information


Activated NTRK3 signals through PI3K / Regulation of gap junction activity / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / Nuclear signaling by ERBB4 / Signaling by EGFR / DCC mediated attractive signaling / VEGFR2 mediated cell proliferation / PECAM1 interactions / Ephrin signaling ...Activated NTRK3 signals through PI3K / Regulation of gap junction activity / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / Nuclear signaling by ERBB4 / Signaling by EGFR / DCC mediated attractive signaling / VEGFR2 mediated cell proliferation / PECAM1 interactions / Ephrin signaling / MET activates PTK2 signaling / Signaling by ERBB2 / Regulation of KIT signaling / GAB1 signalosome / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Co-stimulation by CD28 / Downregulation of ERBB4 signaling / Downstream signal transduction / EPH-ephrin mediated repulsion of cells / Spry regulation of FGF signaling / EPHB-mediated forward signaling / Signaling by SCF-KIT / Regulation of RUNX3 expression and activity / FCGR activation / Thrombin signalling through proteinase activated receptors (PARs) / Cyclin D associated events in G1 / RAF activation / regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / Integrin signaling / cellular response to prolactin / p130Cas linkage to MAPK signaling for integrins / positive regulation of male germ cell proliferation / MAP2K and MAPK activation / dendritic filopodium / Recycling pathway of L1 / Extra-nuclear estrogen signaling / CLEC7A (Dectin-1) signaling / negative regulation of telomere maintenance / response to mineralocorticoid / PIP3 activates AKT signaling / RHO GTPases Activate Formins / positive regulation of dephosphorylation / G alpha (i) signalling events / positive regulation of protein transport / cellular response to progesterone stimulus / BMP receptor binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / ADP signalling through P2Y purinoceptor 1 / RET signaling / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / positive regulation of glucose metabolic process / transcytosis / osteoclast development / connexin binding / VEGFA-VEGFR2 Pathway / focal adhesion assembly / cellular response to fluid shear stress / adherens junction organization / branching involved in mammary gland duct morphogenesis / response to acidic pH / positive regulation of Ras protein signal transduction / positive regulation of podosome assembly / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of lamellipodium morphogenesis / myoblast proliferation / cellular response to peptide hormone stimulus / negative regulation of mitochondrial depolarization / podosome / odontogenesis / cellular response to fatty acid / postsynaptic specialization, intracellular component / regulation of early endosome to late endosome transport / phospholipase activator activity / phosphorylation / oogenesis / interleukin-6-mediated signaling pathway / positive regulation of smooth muscle cell migration / DNA biosynthetic process / positive regulation of Notch signaling pathway / stress fiber assembly / negative regulation of intrinsic apoptotic signaling pathway / uterus development / regulation of cell-cell adhesion / phospholipase binding / regulation of heart rate by cardiac conduction / neurotrophin TRK receptor signaling pathway / dendritic growth cone / platelet-derived growth factor receptor signaling pathway / negative regulation of anoikis / positive regulation of epithelial cell migration
Similarity search - Function
: / 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 / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Proto-oncogene tyrosine-protein kinase Src / Tyrosine-protein kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41795770496 Å
Authorsvon Raussendorf, F. / Leonard, T.A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP28135 Austria
CitationJournal: Sci Rep / Year: 2017
Title: A switch in nucleotide affinity governs activation of the Src and Tec family kinases.
Authors: von Raussendorf, F. / de Ruiter, A. / Leonard, T.A.
History
DepositionNov 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4893
Polymers52,0381
Non-polymers4522
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-15 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.011, 82.974, 105.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tyrosine-protein kinase


Mass: 52037.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Src / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q3UKD6, UniProt: P05480*PLUS, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 50 mM PIPES, pH 6.5 1.2 M sodium tartrate 20 mM DTT 2 mM ADP 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.41→65 Å / Num. obs: 17674 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 34.3898947591 Å2 / Net I/σ(I): 6.1
Reflection shellResolution: 2.41→2.51 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2SRC

2src


Resolution: 2.41795770496→52.5255 Å / SU ML: 0.319898435617 / Cross valid method: FREE R-VALUE / σ(F): 1.34358350621 / Phase error: 26.1574771142
RfactorNum. reflection% reflection
Rfree0.267642283351 872 4.96979368517 %
Rwork0.20792467656 --
obs0.210911359312 17546 99.2870076958 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.8213953531 Å2
Refinement stepCycle: LAST / Resolution: 2.41795770496→52.5255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 28 83 3729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002362028588543733
X-RAY DIFFRACTIONf_angle_d0.582911199215065
X-RAY DIFFRACTIONf_chiral_restr0.0396140306002545
X-RAY DIFFRACTIONf_plane_restr0.00203946487862646
X-RAY DIFFRACTIONf_dihedral_angle_d14.20681807542234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.418-2.56940.3522938454521270.3028496381482763X-RAY DIFFRACTION99.72394755
2.5694-2.76780.3540498224181480.2820293452392677X-RAY DIFFRACTION98.1584433634
2.7678-3.04630.3038767366751460.2428462014922766X-RAY DIFFRACTION99.897084048
3.0463-3.48710.2495055815491570.2008966339012746X-RAY DIFFRACTION99.5883361921
3.4871-4.3930.2416982413661420.1706643458422788X-RAY DIFFRACTION99.1875423155
4.393-52.53790.2376402143371520.1822854461922934X-RAY DIFFRACTION99.2282958199
Refinement TLS params.Method: refined / Origin x: 22.2912602708 Å / Origin y: 83.5075020806 Å / Origin z: 119.521164903 Å
111213212223313233
T0.213220336045 Å20.00110651740131 Å2-0.0568881943948 Å2-0.223449865614 Å20.0108353347993 Å2--0.225287880619 Å2
L1.42813867855 °20.129038436207 °2-0.373951217883 °2-0.94482126093 °2-0.243942630502 °2--1.21421885929 °2
S-0.0270908313887 Å °-0.0966256543793 Å °-0.120483612535 Å °-0.0151274879828 Å °0.0132101507147 Å °0.0292046719676 Å °0.152990772501 Å °0.00180994083774 Å °0.0162422916 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 82 through 529)

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