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Yorodumi- PDB-2o2m: Solution structure of the anti-apoptotic protein Bcl-xL in comple... -
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-Basic information
Entry | Database: PDB / ID: 2o2m | ||||||
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Title | Solution structure of the anti-apoptotic protein Bcl-xL in complex with an acyl-sulfonamide-based ligand | ||||||
Components | Apoptosis regulator Bcl-X | ||||||
Keywords | APOPTOSIS / complex / bcl | ||||||
Function / homology | Function and homology information apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process ...apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / regulation of growth / negative regulation of protein localization to plasma membrane / Bcl-2 family protein complex / BH domain binding / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / epithelial cell proliferation / negative regulation of autophagy / cellular response to amino acid stimulus / release of cytochrome c from mitochondria / regulation of cytokinesis / regulation of mitochondrial membrane potential / response to cytokine / cellular response to gamma radiation / synaptic vesicle membrane / RAS processing / endocytosis / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / nuclear membrane / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Bruncko, M. / Oost, T.K. / Belli, B.A. / Ding, H. / Joseph, M.K. / Kunzer, A. / Martineau, D. / McClellan, W.J. / Mitten, M. / Ng, S.C. ...Bruncko, M. / Oost, T.K. / Belli, B.A. / Ding, H. / Joseph, M.K. / Kunzer, A. / Martineau, D. / McClellan, W.J. / Mitten, M. / Ng, S.C. / Nimmer, P.M. / Oltersdorf, T. / Park, C.M. / Petros, A.M. / Shoemaker, A.R. / Song, X. / Wang, X. / Wendt, M.D. / Zhang, H. / Fesik, S.W. / Rosenberg, S.H. / Elmore, S.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Studies Leading to Potent, Dual Inhibitors of Bcl-2 and Bcl-xL. Authors: Bruncko, M. / Oost, T.K. / Belli, B.A. / Ding, H. / Joseph, M.K. / Kunzer, A. / Martineau, D. / McClellan, W.J. / Mitten, M. / Ng, S.C. / Nimmer, P.M. / Oltersdorf, T. / Park, C.M. / Petros, ...Authors: Bruncko, M. / Oost, T.K. / Belli, B.A. / Ding, H. / Joseph, M.K. / Kunzer, A. / Martineau, D. / McClellan, W.J. / Mitten, M. / Ng, S.C. / Nimmer, P.M. / Oltersdorf, T. / Park, C.M. / Petros, A.M. / Shoemaker, A.R. / Song, X. / Wang, X. / Wendt, M.D. / Zhang, H. / Fesik, S.W. / Rosenberg, S.H. / Elmore, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o2m.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o2m.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 2o2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o2m_validation.pdf.gz | 393.1 KB | Display | wwPDB validaton report |
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Full document | 2o2m_full_validation.pdf.gz | 393.1 KB | Display | |
Data in XML | 2o2m_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 2o2m_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/2o2m ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o2m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16085.890 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07817 |
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#2: Chemical | ChemComp-LI0 / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 13C-SEPARATED NOESY |
-Sample preparation
Details | Contents: 50mM sodium phosphate buffer; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50 mM sodium phosphate / pH: 7 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software | Name: CNS / Developer: Brunger A. T. etall / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: average-minimized |
NMR ensemble | Conformers submitted total number: 1 |