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Yorodumi- PDB-2o1y: Solution structure of the anti-apoptotic protein Bcl-xL in comple... -
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-Basic information
Entry | Database: PDB / ID: 2o1y | ||||||
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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-XBcl-2-like protein 1 | ||||||
Keywords | APOPTOSIS / complex / bcl | ||||||
Function / homology | Function and homology information apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / 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 dendritic cell apoptotic process / negative regulation of execution phase of apoptosis ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / 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 dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / apoptotic mitochondrial changes / germ cell development / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced 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 / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / defense response to virus / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / in utero embryonic development / mitochondrial inner membrane / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytosol / cytoplasm 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 | 2o1y.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o1y.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 2o1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/2o1y ftp://data.pdbj.org/pub/pdb/validation_reports/o1/2o1y | HTTPS FTP |
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-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: 20804.918 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-43B / |
-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: 7.0 / 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 |