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- PDB-5xp7: C-Src in complex with ATP-CHCl -

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Basic information

Entry
Database: PDB / ID: 5xp7
TitleC-Src in complex with ATP-CHCl
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / kinase
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-8C6 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.012 Å
AuthorsGuo, M. / Dai, S. / Duan, Y. / Chen, L. / Chen, Y.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Remarkably Stereospecific Utilization of ATP alpha , beta-Halomethylene Analogues by Protein Kinases.
Authors: Ni, F. / Kung, A. / Duan, Y. / Shah, V. / Amador, C.D. / Guo, M. / Fan, X. / Chen, L. / Chen, Y. / McKenna, C.E. / Zhang, C.
History
DepositionJun 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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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)66,5137
Polymers65,4532
Non-polymers1,0605
Water7,188399
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2113
Polymers32,7271
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area12920 Å2
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3034
Polymers32,7271
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-8 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.276, 63.978, 74.003
Angle α, β, γ (deg.)101.03, 89.83, 90.60
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: 32726.645 Da / Num. of mol.: 2 / Fragment: UNP residues 251-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-8C6 / [(R)-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]-chloranyl-methyl]phosphonic acid


Mass: 459.673 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H16ClN5O9P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→36.6 Å / Num. obs: 48688 / % possible obs: 96.46 % / Redundancy: 3.9 % / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.012→36.551 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.49
RfactorNum. reflection% reflection
Rfree0.1982 2013 4.14 %
Rwork0.1679 --
obs0.1692 48676 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.012→36.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 6 399 4747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014453
X-RAY DIFFRACTIONf_angle_d1.2056042
X-RAY DIFFRACTIONf_dihedral_angle_d13.611669
X-RAY DIFFRACTIONf_chiral_restr0.056650
X-RAY DIFFRACTIONf_plane_restr0.007765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.012-2.06240.28481310.2332908X-RAY DIFFRACTION85
2.0624-2.11810.24991450.21173379X-RAY DIFFRACTION97
2.1181-2.18040.23281400.19793351X-RAY DIFFRACTION97
2.1804-2.25080.23631430.20023357X-RAY DIFFRACTION97
2.2508-2.33120.2921510.19893375X-RAY DIFFRACTION98
2.3312-2.42450.22391400.18633328X-RAY DIFFRACTION97
2.4245-2.53490.20731440.18073390X-RAY DIFFRACTION98
2.5349-2.66850.21761500.17723410X-RAY DIFFRACTION98
2.6685-2.83560.20971460.17753360X-RAY DIFFRACTION98
2.8356-3.05440.23061490.18043401X-RAY DIFFRACTION98
3.0544-3.36160.2131440.17493363X-RAY DIFFRACTION98
3.3616-3.84760.17591470.15473393X-RAY DIFFRACTION98
3.8476-4.84580.15831400.13563286X-RAY DIFFRACTION96
4.8458-36.55740.16521430.15383362X-RAY DIFFRACTION97
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)
10.17740.0434-0.05322.59021.62323.6262-0.0926-0.20950.12550.98740.13510.04430.2443-0.2219-0.04570.75320.0161-0.02950.4547-0.01570.32177.293910.980348.837
21.2428-0.5686-0.31663.42261.57592.5886-0.0547-0.16830.10720.54890.0384-0.17450.249-0.0369-0.00750.2661-0.0324-0.02960.19990.01430.19138.86585.177234.8207
34.14440.50780.85681.70150.04623.36450.0111-0.1558-0.20930.516-0.11660.46630.3374-0.61080.18670.38-0.04040.12360.3987-0.05590.4291-9.0395.479831.6513
42.3071-0.5694-0.62234.2010.15712.12890.02380.3275-0.0229-0.2047-0.2070.4045-0.028-0.36160.11530.178-0.0475-0.01580.2765-0.04870.20310.84331.249318.4332
50.6024-1.6796-0.55535.12271.78842.99090.04280.12190.5902-1.11640.4604-0.395-1.81440.0162-0.35081.30910.1296-0.02440.6946-0.02610.50417.5951-18.4184-8.0905
67.1361-1.8262-0.9526.2626-0.193.41810.00510.54220.941-0.6820.1135-0.7452-1.21180.3751-0.07541.0424-0.1188-0.02720.672-0.06240.44913.727-21.3355-5.5344
71.21450.3721-0.08113.7016-0.09472.4181-0.0190.13550.0982-0.68990.04010.2516-0.0596-0.0512-0.04090.26490.0444-0.05330.221-0.00230.22847.3653-27.71087.2281
84.20121.00442.23421.4987-0.27913.39320.0280.1718-0.3081-0.4438-0.0052-0.57370.0540.4550.04520.27190.03540.08150.35170.01410.421325.1923-26.583810.854
91.89340.7294-0.31414.30740.40591.25420.0708-0.2869-0.06320.1934-0.1478-0.27180.02260.18350.06210.16730.0343-0.02040.24750.04440.181914.8644-30.577824.4092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 257 through 324 )
2X-RAY DIFFRACTION2chain 'A' and (resid 325 through 402 )
3X-RAY DIFFRACTION3chain 'A' and (resid 403 through 440 )
4X-RAY DIFFRACTION4chain 'A' and (resid 441 through 533 )
5X-RAY DIFFRACTION5chain 'B' and (resid 256 through 286 )
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 316 )
7X-RAY DIFFRACTION7chain 'B' and (resid 317 through 402 )
8X-RAY DIFFRACTION8chain 'B' and (resid 403 through 440 )
9X-RAY DIFFRACTION9chain 'B' and (resid 441 through 533 )

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