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- PDB-3svv: Crystal Structure of T338C c-Src covalently bound to vinylsulfona... -

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Basic information

Entry
Database: PDB / ID: 3svv
TitleCrystal Structure of T338C c-Src covalently bound to vinylsulfonamide-pyrazolopyrimidine 9
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / covalently bound ligand / cysteine gatekeeper / Src / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Recycling pathway of L1 / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / regulation of cell cycle / cell adhesion / cell cycle / phosphorylation / signaling receptor binding / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / 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 ...SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / 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 / 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 Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-VSP / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.204 Å
AuthorsGarske, A.L. / Peters, U. / Cortesi, A. / Perez, J. / Shokat, K.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Chemical genetic strategy for targeting protein kinases based on covalent complementarity.
Authors: Garske, A.L. / Peters, U. / Cortesi, A.T. / Perez, J.L. / Shokat, K.M.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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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
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2064
Polymers65,4572
Non-polymers7492
Water4,216234
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1032
Polymers32,7291
Non-polymers3741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1032
Polymers32,7291
Non-polymers3741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.300, 63.315, 74.230
Angle α, β, γ (deg.)78.930, 87.700, 87.920
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 32728.684 Da / Num. of mol.: 2 / Fragment: kinase domain, UNP residues 251-533 / Mutation: T338C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-VSP / N-(3-{[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]methyl}phenyl)ethanesulfonamide


Mass: 374.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N6O2S / Details: chemically synthesized
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsINTERACTION BETWEEN THE LIGAND AND THE PROTEIN RESULTS IN THE CHANGE OF BOND ORDER FROM DOUBLE TO ...INTERACTION BETWEEN THE LIGAND AND THE PROTEIN RESULTS IN THE CHANGE OF BOND ORDER FROM DOUBLE TO SINGLE BOND BETWEEN THE REACTING CARBON AND THE PENULTIMATE ONE.

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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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, 50mM NaOAc, 4-8% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0088 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2010
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / % possible obs: 97.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Χ2: 1.019 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.241.90.2735750.938195.4
2.24-2.281.90.23836841.049196.9
2.28-2.321.90.21836431.029195.7
2.32-2.3720.18336381.048195.9
2.37-2.4220.17436771.037197.3
2.42-2.4820.15337131.047195.7
2.48-2.5420.13737001.018198.3
2.54-2.6120.13536741.047197
2.61-2.6820.12136891.054196.9
2.68-2.7720.10637081.049197.5
2.77-2.8720.09937741197.3
2.87-2.9920.08736811.049197.4
2.99-3.1220.08236680.997197.7
3.12-3.2920.07436781.036197
3.29-3.4920.06637611.002197.8
3.49-3.7620.0637171.029198
3.76-4.141.90.05437010.995197.5
4.14-4.731.90.04937030.975197.8
4.73-5.961.90.04637640.953198.8
5.96-3020.0437881.02199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.08 Å
Translation2.5 Å29.08 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.2.4phasing
PHENIXdev_538refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1yoj

1yoj


Resolution: 2.204→29.08 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8609 / SU ML: 0.24 / σ(F): 0.01 / Phase error: 21.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2153 1991 5.52 %
Rwork0.1758 --
obs0.178 36099 94.76 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.094 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 190.86 Å2 / Biso mean: 20.4704 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-17.6783 Å21.1955 Å21.1685 Å2
2--8.5816 Å24.7788 Å2
3---17.9281 Å2
Refinement stepCycle: LAST / Resolution: 2.204→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4102 0 52 234 4388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124257
X-RAY DIFFRACTIONf_angle_d1.2295775
X-RAY DIFFRACTIONf_chiral_restr0.076618
X-RAY DIFFRACTIONf_plane_restr0.005733
X-RAY DIFFRACTIONf_dihedral_angle_d17.621601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2036-2.28240.24141870.1993071325886
2.2824-2.37370.23111770.18443229340689
2.3737-2.48170.24581970.17673334353192
2.4817-2.61240.20191770.18033371354894
2.6124-2.7760.26492090.19183421363095
2.776-2.99010.22172170.19163474369196
2.9901-3.29070.21071980.18623497369598
3.2907-3.7660.20332110.17933579379099
3.766-4.74140.19822110.15283544375599
4.7414-29.08270.20712070.16793588379599
Refinement TLS params.Method: refined / Origin x: -10.3373 Å / Origin y: 32.497 Å / Origin z: -12.2588 Å
111213212223313233
T-0.0809 Å20.0035 Å20.0339 Å2--0.1217 Å20.039 Å2---0.0769 Å2
L0.0111 °20.0081 °20.0024 °2-0.0556 °20.0162 °2--0.0099 °2
S-0.0291 Å °-0.0825 Å °0.0839 Å °-0.0235 Å °-0.0641 Å °-0.0277 Å °-0.0023 Å °-0.0495 Å °-0.2396 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA257 - 533
2X-RAY DIFFRACTION1allA600
3X-RAY DIFFRACTION1allB256 - 533
4X-RAY DIFFRACTION1allB600
5X-RAY DIFFRACTION1allB1 - 234

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