+Open data
-Basic information
Entry | Database: PDB / ID: 6xlo | ||||||
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Title | Crystal structure of bRaf in complex with inhibitor | ||||||
Components | Serine/threonine-protein kinase B-raf | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | IODIDE ION / Chem-V5J Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å | ||||||
Authors | Yin, J. / Eigenbrot, C. / Wang, W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Targeting KRAS Mutant Cancers via Combination Treatment: Discovery of a 5-Fluoro-4-(3 H )-quinazolinone Aryl Urea pan-RAF Kinase Inhibitor. Authors: Huestis, M.P. / Dela Cruz, D. / DiPasquale, A.G. / Durk, M.R. / Eigenbrot, C. / Gibbons, P. / Gobbi, A. / Hunsaker, T.L. / La, H. / Leung, D.H. / Liu, W. / Malek, S. / Merchant, M. / Moffat, ...Authors: Huestis, M.P. / Dela Cruz, D. / DiPasquale, A.G. / Durk, M.R. / Eigenbrot, C. / Gibbons, P. / Gobbi, A. / Hunsaker, T.L. / La, H. / Leung, D.H. / Liu, W. / Malek, S. / Merchant, M. / Moffat, J.G. / Muli, C.S. / Orr, C.J. / Parr, B.T. / Shanahan, F. / Sneeringer, C.J. / Wang, W. / Yen, I. / Yin, J. / Siu, M. / Rudolph, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xlo.cif.gz | 222.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xlo.ent.gz | 177.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xlo_validation.pdf.gz | 941.7 KB | Display | wwPDB validaton report |
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Full document | 6xlo_full_validation.pdf.gz | 949 KB | Display | |
Data in XML | 6xlo_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 6xlo_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/6xlo ftp://data.pdbj.org/pub/pdb/validation_reports/xl/6xlo | HTTPS FTP |
-Related structure data
Related structure data | 7k0vC 3c4cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32832.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-IOD / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 18% PEG 3350, and 0.2M Na Nitrate, and 0.1 M bis-Tris propane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→56.73 Å / Num. obs: 19111 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.02 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.104 / Rrim(I) all: 0.193 / Net I/σ(I): 6.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C4C Resolution: 2.493→56.73 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.823 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.73 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.316
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Displacement parameters | Biso max: 74.99 Å2 / Biso mean: 30.69 Å2 / Biso min: 6.5 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.493→56.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.493→2.52 Å / Rfactor Rfree error: 0
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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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