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Open data
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Basic information
Entry | Database: PDB / ID: 4bpi | ||||||||||||
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Title | Mcl-1 bound to alpha beta Puma BH3 peptide 2 | ||||||||||||
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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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 63.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446 KB | Display | ![]() |
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Full document | ![]() | 448.3 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bpjC ![]() 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
#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: 2235.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#3: Chemical | ChemComp-CD / #4: Water | ChemComp-HOH / | Sequence details | CHIMERA WITH MOUSE MCL-1 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 51.3 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1M HEPES, PH7.5 1M SODIUM ACETATE, 0.05M CADMIUM SULPHATE |
-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: 1.265106 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18.69 Å / Num. obs: 11279 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 10.09 % / Biso Wilson estimate: 37.16 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.88 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.95 / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NL9 Resolution: 1.982→18.688 Å / SU ML: 0.17 / σ(F): 2.04 / Phase error: 27.56 / 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: 1.982→18.688 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: 7.1676 Å / Origin y: -13.5078 Å / Origin z: 8.2027 Å
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Refinement TLS group | Selection details: ALL |