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Open data
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Basic information
Entry | Database: PDB / ID: 4bpj | ||||||||||||
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Title | Mcl-1 bound to alpha beta Puma BH3 peptide 3 | ||||||||||||
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![]() | APOPTOSIS / CHIMERA / BIM | ||||||||||||
Function / homology | ![]() positive regulation of establishment of protein localization to mitochondrion / BH domain binding / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination ...positive regulation of establishment of protein localization to mitochondrion / BH domain binding / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / positive regulation of cysteine-type endopeptidase activity / positive regulation of thymocyte apoptotic process / channel activity / fibroblast apoptotic process / execution phase of apoptosis / mitochondrial fusion / Bcl-2 family protein complex / Activation of PUMA and translocation to mitochondria / FOXO-mediated transcription of cell death genes / BH3 domain binding / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / response to endoplasmic reticulum stress / negative regulation of autophagy / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / response to cytokine / cellular response to ionizing radiation / determination of adult lifespan / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by ALK fusions and activated point mutants / cellular response to hypoxia / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Smith, B.J. / Lee, E.F. / Checco, J.W. / Gellman, S.H. / Fairlie, W.D. | ||||||||||||
![]() | ![]() Title: Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity for Bcl-2 Family Prosurvival Proteins. Authors: Smith, B.J. / Lee, E.F. / Checco, J.W. / Evangelista, M. / Gellman, S.H. / Fairlie, W.D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.1 KB | Display | ![]() |
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PDB format | ![]() | 71.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
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Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bpiC ![]() 4bpkC ![]() 2nl9S 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18227.592 Da / Num. of mol.: 1 Fragment: FUSION PROTEIN OF MOUSE MCL-1, RESIDUES 152-189 AND HUMAN MCL-1 RESIDUES, 209-327 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: PGEX6P3 / Production host: ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 2104.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Sequence details | CHIMERA WITH MOUSE MCL-1 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 36.9 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.2M IMADAZOLE, PH7.0 0.2M ZINC ACETATE |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 11, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.26511 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.69 Å / Num. obs: 24069 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.57 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.78 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.53 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NL9 Resolution: 1.599→19.693 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 25.1 / 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: 1.599→19.693 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.0196 Å / Origin y: 18.1289 Å / Origin z: 8.5538 Å
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Refinement TLS group | Selection details: ALL |