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- PDB-3zln: Crystal structure of BCL-XL in complex with inhibitor (Compound 3) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zln | ||||||
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Title | Crystal structure of BCL-XL in complex with inhibitor (Compound 3) | ||||||
![]() | BCL-2-LIKE PROTEIN 1 | ||||||
![]() | APOPTOSIS / INHIBITOR | ||||||
Function / homology | ![]() 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 / negative regulation of protein localization to plasma membrane / 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 / 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 / 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 / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Czabotar, P.E. / Lessene, G.L. / Smith, B.J. / Colman, P.M. | ||||||
![]() | ![]() Title: Structure-Guided Design of a Selective Bcl-Xl Inhibitor Authors: Lessene, G.L. / Czabotar, P.E. / Sleebs, B.E. / Zobel, K. / Lowes, K.L. / Adams, J.M. / Baell, J.B. / Colman, P.M. / Deshayes, K. / Fairbrother, W.J. / Flygare, J.A. / Gibbons, P. / Kersten, ...Authors: Lessene, G.L. / Czabotar, P.E. / Sleebs, B.E. / Zobel, K. / Lowes, K.L. / Adams, J.M. / Baell, J.B. / Colman, P.M. / Deshayes, K. / Fairbrother, W.J. / Flygare, J.A. / Gibbons, P. / Kersten, W.J.A. / Kulasegaram, S. / Moss, R.M. / Parisot, J.P. / Smith, B.J. / Street, I.P. / Yang, H. / Huang, D.C.S. / Watson, K.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50 KB | Display | ![]() |
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PDB format | ![]() | 33.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 751.7 KB | Display | ![]() |
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Full document | ![]() | 752.9 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zk6SC ![]() 3zloC ![]() 3zlrC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20804.918 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-44 AND 85-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-H0Y / | ||||
#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | RESIDUES 45 TO 84 REMOVED, LAST 25 RESIDUES TRUNCATED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.01 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 1.8 M (NH4)2 SO4, 40 MM MG2 SO4, 10 MM TRIS PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Date: Oct 25, 2006 / Details: MEECO CAPILLARY |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. obs: 11658 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.95 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.75 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZK6 CHAIN A Resolution: 2.288→31.682 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 23.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.288→31.682 Å
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Refine LS restraints |
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LS refinement shell |
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