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Open data
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Basic information
Entry | Database: PDB / ID: 6qyk | |||||||||
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Title | Structure of MBP-Mcl-1 in complex with compound 7a | |||||||||
![]() | Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1 | |||||||||
![]() | APOPTOSIS / Apoptosis-inhibitor complex / Mcl1 / Small molecule inhibitor / MBP | |||||||||
Function / homology | ![]() positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH domain binding / detection of maltose stimulus / maltose transport complex / BH3 domain binding ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH domain binding / detection of maltose stimulus / maltose transport complex / BH3 domain binding / carbohydrate transport / negative regulation of anoikis / carbohydrate transmembrane transporter activity / protein transmembrane transporter activity / maltose binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / maltose transport / 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 / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / periplasmic space / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dokurno, P. / Szlavik, Z. / Ondi, L. / Csekei, M. / Paczal, A. / Szabo, Z.B. / Radics, G. / Murray, J. / Davidson, J. / Chen, I. ...Dokurno, P. / Szlavik, Z. / Ondi, L. / Csekei, M. / Paczal, A. / Szabo, Z.B. / Radics, G. / Murray, J. / Davidson, J. / Chen, I. / Davis, B. / Hubbard, R.E. / Pedder, C. / Surgenor, A.E. / Smith, J. / Robertson, A. / LeToumelin-Braizat, G. / Cauquil, N. / Zarka, M. / Demarles, D. / Perron-Sierra, F. / Geneste, O. / Kotschy, A. | |||||||||
![]() | ![]() Title: Structure-Guided Discovery of a Selective Mcl-1 Inhibitor with Cellular Activity. Authors: Szlavik, Z. / Ondi, L. / Csekei, M. / Paczal, A. / Szabo, Z.B. / Radics, G. / Murray, J. / Davidson, J. / Chen, I. / Davis, B. / Hubbard, R.E. / Pedder, C. / Dokurno, P. / Surgenor, A. / ...Authors: Szlavik, Z. / Ondi, L. / Csekei, M. / Paczal, A. / Szabo, Z.B. / Radics, G. / Murray, J. / Davidson, J. / Chen, I. / Davis, B. / Hubbard, R.E. / Pedder, C. / Dokurno, P. / Surgenor, A. / Smith, J. / Robertson, A. / LeToumelin-Braizat, G. / Cauquil, N. / Zarka, M. / Demarles, D. / Perron-Sierra, F. / Claperon, A. / Colland, F. / 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 | ![]() | 120.6 KB | Display | ![]() |
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PDB format | ![]() | 88.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qxjC ![]() 6qylC ![]() 6qynC ![]() 6qyoC ![]() 6qypC ![]() 6qz5C ![]() 6qz6C ![]() 6qz7C ![]() 6qz8C ![]() 6qzbC ![]() 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 Source method: isolated from a genetically manipulated source Details: Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820) ...Details: Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with Mcl-1 (UNP Q07820),Protein is a fusion of MBP (UNP P0AEY0) with 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-JLB / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.2 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG3350, 0.2M MAGNESIUM FORMATE, 1MM MALTOSE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 27, 2017 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→28.9 Å / Num. obs: 23650 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.9 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5lof Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.229 / SU ML: 0.218 / SU R Cruickshank DPI: 0.5022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.279 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.61 Å2 / Biso mean: 41.087 Å2 / Biso min: 18.72 Å2
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Refinement step | Cycle: final / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.421 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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