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- PDB-6zie: Crystal structure of MCL-1 in complex with a neutralizing Alphabo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zie | ||||||
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Title | Crystal structure of MCL-1 in complex with a neutralizing Alphabody CMPX-383B | ||||||
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![]() | ANTITUMOR PROTEIN / de novo protein design / 3 helical antiparallel coiled coil / cell penetrating Alphabody MCL-1 neutralizing Alphabody | ||||||
Function / homology | ![]() positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | synthetic construct (others)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pannecoucke, E. / Savvides, S.N. / Desmet, J. / Lasters, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting. Authors: Pannecoucke, E. / Van Trimpont, M. / Desmet, J. / Pieters, T. / Reunes, L. / Demoen, L. / Vuylsteke, M. / Loverix, S. / Vandenbroucke, K. / Alard, P. / Henderikx, P. / Deroo, S. / Baatz, F. ...Authors: Pannecoucke, E. / Van Trimpont, M. / Desmet, J. / Pieters, T. / Reunes, L. / Demoen, L. / Vuylsteke, M. / Loverix, S. / Vandenbroucke, K. / Alard, P. / Henderikx, P. / Deroo, S. / Baatz, F. / Lorent, E. / Thiolloy, S. / Somers, K. / McGrath, Y. / Van Vlierberghe, P. / Lasters, I. / Savvides, S.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.8 KB | Display | ![]() |
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PDB format | ![]() | 97.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.6 KB | Display | ![]() |
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Full document | ![]() | 444.1 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zl1C ![]() 3mk8S 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: 14950.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 18350.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 58.17 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2% (w/v) PEG 3000 0.1 M sodium acetate pH 5.5 0.2 M zinc acetate dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.33 Å / Num. obs: 17660 / % possible obs: 99.68 % / Redundancy: 8.9 % / Biso Wilson estimate: 55.8 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1112 / Rpim(I) all: 0.03928 / Rrim(I) all: 0.1181 / Net I/σ(I): 14.61 |
Reflection shell | Resolution: 2.301→2.383 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1693 / CC1/2: 0.398 / CC star: 0.754 / % possible all: 97.31 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MK8 Resolution: 2.3→44.33 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.274 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.287 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.21
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Displacement parameters | Biso mean: 80.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.32 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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