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Yorodumi- PDB-6fs0: INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN FABCOMPLEX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fs0 | ||||||
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Title | INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN FABCOMPLEX IN COMPLEX WITH AZD5991 | ||||||
Components |
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Keywords | APOPTOSIS / MCL1-FAB4460.55 | ||||||
Function / homology | Function and homology information positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Hargreaves, D. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Discovery of Mcl-1-specific inhibitor AZD5991 and preclinical activity in multiple myeloma and acute myeloid leukemia. Authors: Tron, A.E. / Belmonte, M.A. / Adam, A. / Aquila, B.M. / Boise, L.H. / Chiarparin, E. / Cidado, J. / Embrey, K.J. / Gangl, E. / Gibbons, F.D. / Gregory, G.P. / Hargreaves, D. / Hendricks, J.A. ...Authors: Tron, A.E. / Belmonte, M.A. / Adam, A. / Aquila, B.M. / Boise, L.H. / Chiarparin, E. / Cidado, J. / Embrey, K.J. / Gangl, E. / Gibbons, F.D. / Gregory, G.P. / Hargreaves, D. / Hendricks, J.A. / Johannes, J.W. / Johnstone, R.W. / Kazmirski, S.L. / Kettle, J.G. / Lamb, M.L. / Matulis, S.M. / Nooka, A.K. / Packer, M.J. / Peng, B. / Rawlins, P.B. / Robbins, D.W. / Schuller, A.G. / Su, N. / Yang, W. / Ye, Q. / Zheng, X. / Secrist, J.P. / Clark, E.A. / Wilson, D.M. / Fawell, S.E. / Hird, A.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fs0.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fs0.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 6fs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fs0_validation.pdf.gz | 865.9 KB | Display | wwPDB validaton report |
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Full document | 6fs0_full_validation.pdf.gz | 870.1 KB | Display | |
Data in XML | 6fs0_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 6fs0_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/6fs0 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/6fs0 | HTTPS FTP |
-Related 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: 17984.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820 |
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#2: Antibody | Mass: 22945.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
#3: Antibody | Mass: 22900.178 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
#4: Chemical | ChemComp-E4W / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.58 % / Description: thin small plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M sodium acetate-HCL pH 4.6 18%W/V PEG-8000 0.2M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97858 Å |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Apr 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97858 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→49.32 Å / Num. obs: 29214 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 42.36 Å2 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.24→2.32 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→28.15 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / Rfactor Rfree error: 0.03 / SU R Cruickshank DPI: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.282 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.208
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Displacement parameters | Biso mean: 37.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→28.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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