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- PDB-3tz9: Kinase domain of cSrc in complex with RL130 -

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Basic information

Entry
Database: PDB / ID: 3tz9
TitleKinase domain of cSrc in complex with RL130
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Type II / Allosteric / DFG-out / Drug resistance mutations / Tyrosin-protein kinase / 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-AQU / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsGruetter, C. / Richters, A. / Rauh, D.
CitationJournal: To be Published
Title: Overcoming Gatekeeper Mutations in cSrc and Abl by Hybrid Compound Design
Authors: Richters, A. / Getlik, M. / Gruetter, C. / Schneider, R. / Heuckmann, J.M. / Heynck, S. / Sos, M.L. / Thomas, R.K. / Rauh, D.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)66,4714
Polymers65,4852
Non-polymers9852
Water00
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2352
Polymers32,7431
Non-polymers4931
Water0
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)33,2352
Polymers32,7431
Non-polymers4931
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.020, 63.420, 74.200
Angle α, β, γ (deg.)79.600, 87.890, 89.980
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: 32742.711 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residues 251-533 / Mutation: S345C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC, v-Src sarcoma viral oncogene / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-AQU / 1-[1-(3-aminophenyl)-3-tert-butyl-1H-pyrazol-5-yl]-3-[4-(quinazolin-4-ylamino)phenyl]urea


Mass: 492.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H28N8O

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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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 20000, 15% glycerol, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0039 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 23, 2010 / Details: Dynamically bendable mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0039 Å / Relative weight: 1
ReflectionResolution: 3.1→45 Å / Num. all: 13657 / Num. obs: 12539 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 1.79 % / Biso Wilson estimate: 43.513 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) all% possible all
3.1-3.21.840.4280.205421401245124511660.2993.7
3.2-3.30.2940.1485.111854108810200.2193.8
3.3-3.60.2140.1066.424269258123690.14991.8
3.6-4.40.0980.0639.836312395935660.08990.1
4.4-6.20.070.05112.014939307928250.07391.8
6.2-80.0560.04514.415589068380.06492.5
8-120.0410.03717.38835635300.05394.1
12-160.0280.02522.772541351310.03697
16-450.0320.03223.4179101940.04593.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.77 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å41.99 Å
Translation3.1 Å41.99 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SLS-Softwaredata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F3V

3f3v


Resolution: 3.1→41.99 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.862 / WRfactor Rfree: 0.2867 / WRfactor Rwork: 0.2229 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7805 / SU B: 47.645 / SU ML: 0.393 / SU R Cruickshank DPI: 0.4173 / SU Rfree: 0.5432 / Cross valid method: THROUGHOUT / ESU R Free: 0.542 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2832 815 6.5 %RANDOM
Rwork0.2115 ---
obs0.2162 12538 100 %-
all-13657 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.67 Å2 / Biso mean: 53.022 Å2 / Biso min: 26.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å2-0.72 Å20.77 Å2
2---3.62 Å20.96 Å2
3---4.52 Å2
Refinement stepCycle: LAST / Resolution: 3.1→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4194 0 74 0 4268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224380
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9975940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9923.776196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.49215758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7161530
X-RAY DIFFRACTIONr_chiral_restr0.0860.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023344
X-RAY DIFFRACTIONr_nbd_refined0.240.22049
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3470.22
X-RAY DIFFRACTIONr_mcbond_it0.5461.52667
X-RAY DIFFRACTIONr_mcangle_it0.9824201
X-RAY DIFFRACTIONr_scbond_it1.13932008
X-RAY DIFFRACTIONr_scangle_it1.8644.51739
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 62 -
Rwork0.316 902 -
all-964 -
obs--100 %
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)
10.97130.24090.19581.22550.01841.4091-0.05870.0107-0.0588-0.2115-0.0326-0.022-0.13730.09410.0913-0.11860.01-0.0033-0.12380.0276-0.1182-4.620530.59971.6526
20.7305-0.36440.04431.5877-0.05811.5559-0.09680.00650.01910.3006-0.001-0.0234-0.1052-0.06230.0978-0.0881-0.0092-0.0149-0.13020.0188-0.1057-11.729262.094923.3855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A257 - 533
2X-RAY DIFFRACTION2B257 - 533

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