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- PDB-5w8f: Crystal structure of human Mcl-1 in complex with modified Bim BH3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w8f | |||||||||
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Title | Crystal structure of human Mcl-1 in complex with modified Bim BH3 peptide SAH-MS1-14 | |||||||||
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![]() | PEPTIDE BINDING PROTEIN / Stapled peptide / BCL-2 family / BH3 domain / apoptosis | |||||||||
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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rezaei Araghi, R. / Jenson, J.M. / Grant, R.A. / Keating, A.E. | |||||||||
![]() | ![]() Title: Iterative optimization yields Mcl-1-targeting stapled peptides with selective cytotoxicity to Mcl-1-dependent cancer cells. Authors: Rezaei Araghi, R. / Bird, G.H. / Ryan, J.A. / Jenson, J.M. / Godes, M. / Pritz, J.R. / Grant, R.A. / Letai, A. / Walensky, L.D. / Keating, A.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.7 KB | Display | ![]() |
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PDB format | ![]() | 60.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 442.9 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w89C ![]() 3mk8S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 17150.572 Da / Num. of mol.: 1 / Fragment: UNP residues 172-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 2593.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Reservior : 25% PEG 3350, 50mM Tris pH 9.0, 0.2 M Ammonium acetate; Protein: 408 uM in 20 mM TRis , 10 mM TCEP, 5mM Zn2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.615 Å / Num. obs: 16798 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.84 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.48 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 11.85 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.674 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MK8 Resolution: 1.85→19.62 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.51 / 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: 1.85→19.62 Å
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Refine LS restraints |
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LS refinement shell |
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