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Open data
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Basic information
Entry | Database: PDB / ID: 6ybl | ||||||
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Title | Structure of MBP-Mcl-1 in complex with compound 9m | ||||||
![]() | Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1 | ||||||
![]() | APOPTOSIS / Apoptosis-inhibitor complex / Mcl-1 / S64315 / MBP / small molecule inhibitor | ||||||
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 / detection of maltose stimulus / maltose transport complex / BH3 domain binding / carbohydrate transport ...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 / detection of maltose stimulus / maltose transport complex / BH3 domain binding / carbohydrate transport / carbohydrate transmembrane transporter activity / negative regulation of anoikis / maltose binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / maltose transport / maltodextrin transmembrane transport / protein transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex / negative regulation of autophagy / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / periplasmic space / 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 | ![]() ![]() ![]() | ||||||
![]() | Dokurno, P. / Surgenor, A.E. / Murray, J.B. | ||||||
![]() | ![]() Title: Discovery of S64315, a Potent and Selective Mcl-1 Inhibitor. Authors: Szlavik, Z. / Csekei, M. / Paczal, A. / Szabo, Z.B. / Sipos, S. / Radics, G. / Proszenyak, A. / Balint, B. / Murray, J. / Davidson, J. / Chen, I. / Dokurno, P. / Surgenor, A.E. / Daniels, Z. ...Authors: Szlavik, Z. / Csekei, M. / Paczal, A. / Szabo, Z.B. / Sipos, S. / Radics, G. / Proszenyak, A. / Balint, B. / Murray, J. / Davidson, J. / Chen, I. / Dokurno, P. / Surgenor, A.E. / Daniels, Z.M. / Hubbard, R.E. / Le Toumelin-Braizat, G. / Claperon, A. / Lysiak-Auvity, G. / Girard, A.M. / Bruno, A. / Chanrion, M. / Colland, F. / Maragno, A.L. / Demarles, D. / Geneste, O. / Kotschy, 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 | ![]() | 123.7 KB | Display | ![]() |
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PDB format | ![]() | 91 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ybgC ![]() 6ybjC ![]() 6ybkC ![]() 5lofS 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: 57225.867 Da / Num. of mol.: 1 / Mutation: K194A,K197A,R201A Source method: isolated from a genetically manipulated source Details: Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820) ...Details: Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) and Mcl-1 (UNP Q07820) Source: (gene. exp.) ![]() ![]() ![]() Gene: malE, Z5632, ECs5017, MCL1, BCL2L3 / Production host: ![]() ![]() References: UniProt: P0AEY0, UniProt: Q07820, UniProt: P0AEX9*PLUS |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Chemical | ChemComp-OK5 / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M BisTris buffer pH 6.5, 20% PegMME5K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 35893 / % possible obs: 99.2 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.097 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5585 / CC1/2: 0.712 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LOF Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2066 / WRfactor Rwork: 0.1608 / FOM work R set: 0.8185 / SU B: 5.762 / SU ML: 0.144 / SU R Cruickshank DPI: 0.2187 / SU Rfree: 0.1851 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.92 Å2 / Biso mean: 36.979 Å2 / Biso min: 22.23 Å2
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Refinement step | Cycle: final / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.212 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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