+Open data
-Basic information
Entry | Database: PDB / ID: 6ybj | ||||||
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Title | Structure of MBP-Mcl-1 in complex with compound 3e | ||||||
Components | Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1 | ||||||
Keywords | APOPTOSIS / Apoptosis-inhibitor complex / Mcl-1 / S64315 / MBP / small molecule inhibitor | ||||||
Function / homology | Function and homology information 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 / protein transmembrane transporter activity / maltodextrin transmembrane transport / 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 | Escherichia coli O157:H7 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Dokurno, P. / Surgenor, A.E. / Murray, J.B. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ybj.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ybj.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ybj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ybj_validation.pdf.gz | 880.6 KB | Display | wwPDB validaton report |
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Full document | 6ybj_full_validation.pdf.gz | 889.2 KB | Display | |
Data in XML | 6ybj_validation.xml.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/6ybj ftp://data.pdbj.org/pub/pdb/validation_reports/yb/6ybj | HTTPS FTP |
-Related structure data
Related structure data | 6ybgC 6ybkC 6yblC 5lofS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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),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.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human) Gene: malE, Z5632, ECs5017, MCL1, BCL2L3 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLysS 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-CL / |
#4: Chemical | ChemComp-OJW / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→46.9 Å / Num. obs: 23098 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.34→2.4 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1663 / Rpim(I) all: 0.632 / % possible all: 97.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5lof Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2494 / WRfactor Rwork: 0.1915 / FOM work R set: 0.7991 / SU B: 11.491 / SU ML: 0.236 / SU R Cruickshank DPI: 1.0855 / SU Rfree: 0.2955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.086 / ESU R Free: 0.296 / 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: 158.56 Å2 / Biso mean: 50.851 Å2 / Biso min: 25.72 Å2
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Refinement step | Cycle: final / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.633 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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