+Open data
-Basic information
Entry | Database: PDB / ID: 5bmm | |||||||||
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Title | Src in complex with DNA-templated macrocyclic inhibitor MC25b | |||||||||
Components |
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Keywords | Transferase/transferase Inhibitor / 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 / DCC mediated attractive signaling / GP1b-IX-V activation signalling / 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 / cell adhesion / regulation of cell cycle / 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 | |||||||||
Biological species | Gallus gallus (chicken) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Georghiou, G. / Guja, K.E. / Aleem, S. / Kleiner, R.E. / Liu, D.R. / Miller, W.T. / Garcia-Diaz, M. / Seeliger, M.A. | |||||||||
Citation | Journal: Cell Chem Biol / Year: 2016 Title: Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles. Authors: Aleem, S.U. / Georghiou, G. / Kleiner, R.E. / Guja, K.E. / Craddock, B.P. / Lyczek, A. / Chan, A.I. / Garcia-Diaz, M. / Miller, W.T. / Liu, D.R. / Seeliger, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bmm.cif.gz | 229.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bmm.ent.gz | 184.1 KB | Display | PDB format |
PDBx/mmJSON format | 5bmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/5bmm ftp://data.pdbj.org/pub/pdb/validation_reports/bm/5bmm | HTTPS FTP |
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-Related structure data
Related structure data | 3u4wS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32726.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P00523, non-specific protein-tyrosine kinase #2: Protein/peptide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 14% PEG 5000 MME, 0.3 M NaH2PO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.65 Å / Num. obs: 17499 / % possible obs: 83.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.252 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3 / % possible all: 26.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U4W Resolution: 2.5→42.65 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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