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Yorodumi- PDB-2o21: Solution structure of the anti-apoptotic protein Bcl-2 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o21 | ||||||
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Title | Solution structure of the anti-apoptotic protein Bcl-2 in complex with an acyl-sulfonamide-based ligand | ||||||
Components | Apoptosis regulator Bcl-2 | ||||||
Keywords | APOPTOSIS / complex / bcl | ||||||
Function / homology | Function and homology information negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / digestive tract morphogenesis / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / apoptotic process in bone marrow cell / regulation of cell-matrix adhesion / stem cell development / negative regulation of calcium ion transport into cytosol / T cell apoptotic process / melanocyte differentiation / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / lymphoid progenitor cell differentiation / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / oocyte development / Regulation of MITF-M-dependent genes involved in apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of multicellular organism growth / neuron maturation / metanephros development / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / fertilization / negative regulation of ossification / negative regulation of B cell apoptotic process / response to UV-B / regulation of mitochondrial membrane permeability / regulation of growth / negative regulation of protein localization to plasma membrane / response to iron ion / calcium ion transport into cytosol / motor neuron apoptotic process / negative regulation of mitochondrial depolarization / channel activity / axon regeneration / Bcl-2 family protein complex / epithelial cell apoptotic process / smooth muscle cell migration / BH domain binding / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / organ growth / branching involved in ureteric bud morphogenesis / response to cycloheximide / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / : / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / STAT5 activation downstream of FLT3 ITD mutants / B cell lineage commitment / cellular response to alkaloid / hepatocyte apoptotic process / pore complex / positive regulation of smooth muscle cell migration / B cell proliferation / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / T cell homeostasis / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / regulation of calcium ion transport / B cell homeostasis / humoral immune response / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors 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 | 2o21.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o21.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 2o21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o21_validation.pdf.gz | 395.2 KB | Display | wwPDB validaton report |
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Full document | 2o21_full_validation.pdf.gz | 395.2 KB | Display | |
Data in XML | 2o21_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 2o21_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/2o21 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o21 | 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: 19155.283 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10415, 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: 25mM TRIS buffer; 150 mM sodium chloride; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 25 mM TRIS; 150 mM sodium chloride / pH: 8 / Pressure: 1 atm / Temperature: 298 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 |