+Open data
-Basic information
Entry | Database: PDB / ID: 5mes | ||||||
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Title | MCL1 FAB COMPLEX IN COMPLEX WITH COMPOUND 29 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MCL1 / FAB / macrocycle / MCL1-FAB_55_C6HIS | ||||||
Function / homology | Function and homology information BH domain binding / 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 ...BH domain binding / 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 / 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 | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Hargreaves, D. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Structure Based Design of Non-Natural Peptidic Macrocyclic Mcl-1 Inhibitors. Authors: Johannes, J.W. / Bates, S. / Beigie, C. / Belmonte, M.A. / Breen, J. / Cao, S. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Ferguson, A.D. / Habeshian, S. / Hargreaves, D. ...Authors: Johannes, J.W. / Bates, S. / Beigie, C. / Belmonte, M.A. / Breen, J. / Cao, S. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Ferguson, A.D. / Habeshian, S. / Hargreaves, D. / Joubran, C. / Kazmirski, S. / Keefe, A.D. / Lamb, M.L. / Lan, H. / Li, Y. / Ma, H. / Mlynarski, S. / Packer, M.J. / Rawlins, P.B. / Robbins, D.W. / Shen, H. / Sigel, E.A. / Soutter, H.H. / Su, N. / Troast, D.M. / Wang, H. / Wickson, K.F. / Wu, C. / Zhang, Y. / Zhao, Q. / Zheng, X. / Hird, A.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mes.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mes.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mes_validation.pdf.gz | 808.3 KB | Display | wwPDB validaton report |
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Full document | 5mes_full_validation.pdf.gz | 814.3 KB | Display | |
Data in XML | 5mes_validation.xml.gz | 24 KB | Display | |
Data in CIF | 5mes_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/5mes ftp://data.pdbj.org/pub/pdb/validation_reports/me/5mes | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18227.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: Mcl1, MCL1, BCL2L3 / Production host: Komagataella pastoris (fungus) / References: UniProt: P97287, UniProt: Q07820 |
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#2: Antibody | Mass: 24488.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris (fungus) |
#3: Antibody | Mass: 24157.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris (fungus) |
#4: Chemical | ChemComp-7LT / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 8K 10%w/v, PEG 1500 10%w/v |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→81.02 Å / Num. obs: 27132 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.23 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.057 / Rrim(I) all: 0.083 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.24→2.3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.709 / CC1/2: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→81.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.214
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Displacement parameters | Biso mean: 52.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→81.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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