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- PDB-6vbx: Crystal structure of Mcl-1 in complex with 138E12 peptide, Lys-co... -
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Basic information
Entry | Database: PDB / ID: 6vbx | ||||||
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Title | Crystal structure of Mcl-1 in complex with 138E12 peptide, Lys-covalent antagonist | ||||||
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![]() | APOPTOSIS / MCL-1 / 138E12 peptide / Lys-covalent antagonists | ||||||
Function / homology | ![]() BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / meiosis I / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / cellular homeostasis / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / channel activity / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / BH domain binding / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / odontogenesis of dentin-containing tooth / BH3 domain binding / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / negative regulation of autophagy / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / kidney development / response to cytokine / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / spermatogenesis / microtubule binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pellecchia, M. / Perry, J.J. / Kenjic, N. / Assar, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design, Synthesis, and Structural Characterization of Lysine Covalent BH3 Peptides Targeting Mcl-1. Authors: Gambini, L. / Udompholkul, P. / Baggio, C. / Muralidharan, A. / Kenjic, N. / Assar, Z. / Perry, J.J.P. / Pellecchia, M. #1: Journal: Meth. Enzymol. / Year: 1997 Title: Processing of X-ray diffraction data collected in oscillation mode. Authors: Otwinowski, Z. / Minor, W. #2: Journal: J Appl Crystallogr / Year: 2007 Title: Phaser crystallographic software. Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. / Adams, P.D. / Winn, M.D. / Storoni, L.C. / Read, R.J. #3: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2004 Title: REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Authors: Vagin, A.A. / Steiner, R.A. / Lebedev, A.A. / Potterton, L. / McNicholas, S. / Long, F. / Murshudov, G.N. #4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2004 Title: Coot: model-building tools for molecular graphics. Authors: Paul Emsley / Kevin Cowtan / ![]() Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality ...CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.3 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2nl9S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17850.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1805.020 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This is a chemically synthesized peptide with unnatural ligand (see ligand section) on the N-terminal end. Ligands is covalently attached to Lys234 of chain A. Source: (synth.) synthetic construct (others) / References: UniProt: O43521*PLUS |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5M Potassium Thiocyanate, 0.1M Sodium Acetate:HCL pH4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→34.001 Å / Num. obs: 12721 / % possible obs: 99.75 % / Redundancy: 7.9 % / Biso Wilson estimate: 32.63 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.955→2.025 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1235 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NL9 Resolution: 1.95→34 Å / SU ML: 0.2912 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0423 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.58 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→34 Å
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Refine LS restraints |
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LS refinement shell |
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