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- PDB-5teh: c-Src V281C kinase domain in complex with Rao-IV-156 -

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Basic information

Entry
Database: PDB / ID: 5teh
Titlec-Src V281C kinase domain in complex with Rao-IV-156
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / aC helix out / 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 / CD28 co-stimulation ...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 / CD28 co-stimulation / CTLA4 inhibitory signaling / 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 / progesterone receptor signaling pathway / 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 tyrosine kinase activity / protein phosphatase binding / mitochondrial inner membrane / cell differentiation / cytoskeleton / regulation of cell cycle / cell adhesion / endosome membrane / innate immune response / signaling receptor binding / focal adhesion / 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 / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-S56 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsDieter, E.M. / Merritt, E.A. / Maly, D.J.
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
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
DepositionSep 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: 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.journal_volume / _citation.title
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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)66,4584
Polymers65,4612
Non-polymers9972
Water32418
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2292
Polymers32,7311
Non-polymers4991
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)33,2292
Polymers32,7311
Non-polymers4991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.790, 63.590, 76.070
Angle α, β, γ (deg.)76.730, 89.930, 89.790
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: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 256 - 533 / Label seq-ID: 9 - 286

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-S56 / (2S)-3-[4-amino-7-(2-methoxyethyl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyano-N-(propan-2-yl)propanamide / Rao-IV-156, bound form


Mass: 498.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100 mM MES pH 6.3, 40 mM NaOAc, 8% PEG3350, 10% glycerol, 10 mM DTT

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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: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.417
11h,-k,-l20.583
ReflectionResolution: 3→74.04 Å / Num. obs: 12160 / % possible obs: 79.8 % / Redundancy: 3.4 % / CC1/2: 0.893 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.111 / Rrim(I) all: 0.202 / Net I/σ(I): 6 / Num. measured all: 41021 / Scaling rejects: 324
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.183.50.31718820730.8760.1920.3653.283.6
9-74.043.40.07816014750.970.050.0939.282.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SWH

5swh


Resolution: 2.99→74.04 Å / Cor.coef. Fo:Fc: 0.677 / Cor.coef. Fo:Fc free: 0.59 / SU B: 41.151 / SU ML: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3659 661 5.4 %RANDOM
Rwork0.3036 ---
obs0.3069 11499 78.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.46 Å2 / Biso mean: 77.268 Å2 / Biso min: 47.79 Å2
Baniso -1Baniso -2Baniso -3
1--37.91 Å2-14.19 Å20.46 Å2
2--53.44 Å212.16 Å2
3----15.53 Å2
Refinement stepCycle: final / Resolution: 2.99→74.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 74 18 4292
Biso mean--51.75 51.75 -
Num. residues----523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194385
X-RAY DIFFRACTIONr_bond_other_d0.0030.024151
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.9695936
X-RAY DIFFRACTIONr_angle_other_deg1.15539569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7345519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56623.795195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89515757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.871530
X-RAY DIFFRACTIONr_chiral_restr0.1060.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215090
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02988
Refine LS restraints NCS

Ens-ID: 1 / Number: 15846 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.99→3.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 58 -
Rwork0.276 740 -
all-798 -
obs--71.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0391-0.0177-0.0440.0897-0.12470.32070.0803-0.1807-0.13040.0937-0.0650.0963-0.29320.5402-0.01531.214-0.0934-0.11051.63890.171.1836-8.1219-38.645918.7786
23.37383.4333-1.16574.1191-1.93981.31730.3035-0.1868-0.10780.094-0.09110.02640.1751-0.0832-0.21230.72980.1239-0.11450.62960.15480.8938-15.7642-36.725515.5472
30.02080.0098-0.04090.17380.58982.2787-0.0039-0.11930.00980.0227-0.06840.0530.09070.21590.07220.90050.0924-0.05820.74660.16981.2649-2.9579-33.81112.9979
43.80380.79761.00634.60910.44150.75670.2898-0.5582-0.02230.422-0.29440.17410.1831-0.10420.00460.46780.0969-0.01610.15470.05110.5513-7.0258-28.9045-4.2657
55.3820.13051.16181.84810.57231.6851-0.021-0.4618-0.421-0.1060.1739-0.07750.15560.3633-0.15290.43080.1425-0.05910.21240.04780.77337.1885-34.1487-10.3574
61.271-1.1313-0.65131.76280.1260.6130.09830.1949-0.0004-0.073-0.10960.00190.0082-0.12440.01140.55790.0999-0.08180.0480.01180.9349-1.5074-23.1328-16.767
70.99331.06621.18611.21671.24661.4272-0.08430.0883-0.25390.10540.3819-0.1802-0.18240.0024-0.29751.28660.43780.07451.27810.3971.239-6.1066-72.1264-43.1686
81.72070.16422.91420.03070.3375.20640.02190.154-0.2088-0.0658-0.00340.0531-0.25170.306-0.01850.61650.0429-0.06090.37690.06130.755-1.4236-72.7102-39.9395
90.3082-0.05670.77340.0759-0.23782.105-0.0503-0.0505-0.1325-0.17510.0449-0.17550.0804-0.28880.00541.0011-0.0320.05410.67260.01331.3026-12.2049-65.6918-38.784
100.8265-0.04990.61571.8173-0.35443.8514-0.02840.48620.1903-0.1959-0.0106-0.1321-0.0267-0.11430.03890.43390.0452-0.02990.36230.09910.7386-6.0247-63.2652-25.9894
114.12113.42850.51552.94550.4490.0749-0.1960.36-0.4187-0.40640.1559-0.3134-0.06840.03530.04020.62480.39810.03860.36380.20281.0564-17.0812-63.005-21.9246
122.68271.8216-1.36941.8731-0.83192.6024-0.0535-0.14990.12730.07830.11880.29150.0228-0.2172-0.06530.54970.1392-0.09460.157-0.01151.0314-12.8768-59.7038-9.3813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A256 - 280
2X-RAY DIFFRACTION2A281 - 293
3X-RAY DIFFRACTION3A294 - 348
4X-RAY DIFFRACTION4A349 - 402
5X-RAY DIFFRACTION5A403 - 477
6X-RAY DIFFRACTION6A478 - 533
7X-RAY DIFFRACTION7B256 - 278
8X-RAY DIFFRACTION8B279 - 288
9X-RAY DIFFRACTION9B289 - 321
10X-RAY DIFFRACTION10B322 - 395
11X-RAY DIFFRACTION11B396 - 442
12X-RAY DIFFRACTION12B443 - 533

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