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- PDB-5swh: c-Src V281C kinase domain in complex with Rao-IV-151 -

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Basic information

Entry
Database: PDB / ID: 5swh
Titlec-Src V281C kinase domain in complex with Rao-IV-151
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / active conformation / covalently-linked inihibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / immune system process / progesterone receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / cell junction / cell-cell junction / protein tyrosine kinase activity / protein phosphatase binding / cell differentiation / cytoskeleton / mitochondrial inner membrane / regulation of cell cycle / cell adhesion / endosome membrane / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytosol
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-71D / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMerritt, E.A. / Dieter, E.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM086858 United States
CitationJournal: Mol.Cell / Year: 2019
Title: A combined approach reveals a regulatory mechanism coupling Src's kinase activity, localization, and phosphotransferase-independent functions
Authors: Register, A.C. / Maly, D.J.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 13, 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: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3434
Polymers65,4612
Non-polymers8822
Water1,11762
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1722
Polymers32,7311
Non-polymers4411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1722
Polymers32,7311
Non-polymers4411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.819, 64.139, 74.910
Angle α, β, γ (deg.)77.940, 89.500, 89.830
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 258 - 532 / Label seq-ID: 11 - 285

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 32730.656 Da / Num. of mol.: 2 / Mutation: V281C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-71D / (2R)-3-[4-amino-5-(4-chlorophenyl)-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyano-N-(propan-2-yl)propanami de / Rao-IV-151, bound form


Mass: 440.926 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25ClN6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6, 8% PEG 3350, 3% glycerol, 10 mM DTT, 10 mM NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→73.25 Å / Num. obs: 21164 / % possible obs: 80.3 % / Redundancy: 7.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.075 / Rrim(I) all: 0.201 / Net I/σ(I): 8.5 / Num. measured all: 149393 / Scaling rejects: 98
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.671.2250.577180.8
9.01-73.257.10.0540.997182.7

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3uqg

3uqg


Resolution: 2.5→73.25 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.852 / SU B: 13.64 / SU ML: 0.286 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.798 / ESU R Free: 0.364
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1115 5.3 %RANDOM
Rwork0.241 ---
obs0.2435 19893 79.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 184.64 Å2 / Biso mean: 53.038 Å2 / Biso min: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å20.06 Å20.46 Å2
2---1.48 Å22.62 Å2
3---4.33 Å2
Refinement stepCycle: final / Resolution: 2.5→73.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 62 62 4235
Biso mean--73.59 30.08 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194289
X-RAY DIFFRACTIONr_bond_other_d0.0040.024039
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9675820
X-RAY DIFFRACTIONr_angle_other_deg1.1139304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36323.838185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9215722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4511528
X-RAY DIFFRACTIONr_chiral_restr0.080.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024937
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02955
X-RAY DIFFRACTIONr_mcbond_it3.8495.3672078
X-RAY DIFFRACTIONr_mcbond_other3.8485.3672079
X-RAY DIFFRACTIONr_mcangle_it6.3598.0412589
Refine LS restraints NCS

Ens-ID: 1 / Number: 30252 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 85 -
Rwork0.368 1536 -
all-1621 -
obs--82.33 %

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