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- PDB-6stj: Selective Affimers Recognize BCL-2 Family Proteins Through Non-Ca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6stj | ||||||
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Title | Selective Affimers Recognize BCL-2 Family Proteins Through Non-Canonical Structural Motifs | ||||||
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![]() | PROTEIN BINDING / Affimer | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Hobor, F. / Miles, J.A. / Trinh, C.H. / Taylor, J. / Tiede, C. / Rowell, P.R. / Jackson, B. / Nadat, F. / Kyle, H.F. / Wicky, B.I.M. ...Hobor, F. / Miles, J.A. / Trinh, C.H. / Taylor, J. / Tiede, C. / Rowell, P.R. / Jackson, B. / Nadat, F. / Kyle, H.F. / Wicky, B.I.M. / Clarke, J. / Tomlinson, D.C. / Wilson, A.J. / Edwards, T.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Selective Affimers Recognise the BCL-2 Family Proteins BCL-x L and MCL-1 through Noncanonical Structural Motifs*. Authors: Miles, J.A. / Hobor, F. / Trinh, C.H. / Taylor, J. / Tiede, C. / Rowell, P.R. / Jackson, B.R. / Nadat, F.A. / Ramsahye, P. / Kyle, H.F. / Wicky, B.I.M. / Clarke, J. / Tomlinson, D.C. / ...Authors: Miles, J.A. / Hobor, F. / Trinh, C.H. / Taylor, J. / Tiede, C. / Rowell, P.R. / Jackson, B.R. / Nadat, F.A. / Ramsahye, P. / Kyle, H.F. / Wicky, B.I.M. / Clarke, J. / Tomlinson, D.C. / Wilson, A.J. / Edwards, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 372.8 KB | Display | ![]() |
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PDB format | ![]() | 310.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.3 KB | Display | ![]() |
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Full document | ![]() | 493.2 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6st2C ![]() 4n6tS ![]() 5fc4S 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: 17765.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 10966.528 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% PEG MME 2K, 0.2M ammonium sulfate, 0.1M sodium acetate pH4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→113.1 Å / Num. obs: 57159 / % possible obs: 99.4 % / Redundancy: 11.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.644 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2578 / CC1/2: 0.681 / Rpim(I) all: 0.591 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FC4, 4N6T Resolution: 2.2→113.08 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 20.404 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.238 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.55 Å2 / Biso mean: 61.212 Å2 / Biso min: 31.69 Å2
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Refinement step | Cycle: final / Resolution: 2.2→113.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.254 Å / Rfactor Rfree error: 0
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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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