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Open data
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Basic information
Entry | Database: PDB / ID: 6qfm | ||||||
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Title | Structure of human Mcl-1 in complex with PUMA BH3 peptide | ||||||
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![]() | APOPTOSIS / MCL1 / BCL2 / PUMA | ||||||
Function / homology | ![]() positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / positive regulation of cysteine-type endopeptidase activity ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / positive regulation of cysteine-type endopeptidase activity / positive regulation of thymocyte apoptotic process / channel activity / fibroblast apoptotic process / execution phase of apoptosis / mitochondrial fusion / Bcl-2 family protein complex / Activation of PUMA and translocation to mitochondria / FOXO-mediated transcription of cell death genes / BH3 domain binding / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / response to endoplasmic reticulum stress / negative regulation of autophagy / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / response to cytokine / cellular response to ionizing radiation / determination of adult lifespan / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by ALK fusions and activated point mutants / cellular response to hypoxia / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dokurno, P. / Murray, J. / Davidson, J. / Chen, I. / Davis, B. / Graham, C.J. / Harris, R. / Jordan, A.M. / Matassova, N. / Pedder, C. ...Dokurno, P. / Murray, J. / Davidson, J. / Chen, I. / Davis, B. / Graham, C.J. / Harris, R. / Jordan, A.M. / Matassova, N. / Pedder, C. / Ray, S. / Roughley, S. / Smith, J. / Walmsley, C. / Wang, Y. / Whitehead, N. / Williamson, D.S. / Casara, P. / Le Diguarher, T. / Hickman, J. / Stark, J. / Kotschy, A. / Geneste, O. / Hubbard, R.E. | ||||||
![]() | ![]() Title: Establishing Drug Discovery and Identification of Hit Series for the Anti-apoptotic Proteins, Bcl-2 and Mcl-1. Authors: Murray, J.B. / Davidson, J. / Chen, I. / Davis, B. / Dokurno, P. / Graham, C.J. / Harris, R. / Jordan, A. / Matassova, N. / Pedder, C. / Ray, S. / Roughley, S.D. / Smith, J. / Walmsley, C. / ...Authors: Murray, J.B. / Davidson, J. / Chen, I. / Davis, B. / Dokurno, P. / Graham, C.J. / Harris, R. / Jordan, A. / Matassova, N. / Pedder, C. / Ray, S. / Roughley, S.D. / Smith, J. / Walmsley, C. / Wang, Y. / Whitehead, N. / Williamson, D.S. / Casara, P. / Le Diguarher, T. / Hickman, J. / Stark, J. / Kotschy, A. / Geneste, O. / Hubbard, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.3 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.3 KB | Display | ![]() |
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Full document | ![]() | 445.6 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qfiC ![]() 6qfqC ![]() 6qg8C ![]() 6qgdC ![]() 6qggC ![]() 6qghC ![]() 6qgjC ![]() 6qgkC ![]() 2nl9S 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: 18352.852 Da / Num. of mol.: 1 Mutation: E173D, D241G, L246F, I251V, S255K, T280S, I281V, C286F, S293T, E322Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 2747.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM imidazole buffer pH 7.0, 50 mM zinc acetate and 20-25% polyethylene glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→25 Å / Num. obs: 9678 / % possible obs: 84.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.079 / Χ2: 1.221 / Net I/σ(I): 10.4 / Num. measured all: 31218 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NL9 Resolution: 2→9.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.06 / SU ML: 0.162 / SU R Cruickshank DPI: 0.2679 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.219 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: 88.18 Å2 / Biso mean: 35.187 Å2 / Biso min: 3.83 Å2
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Refinement step | Cycle: final / Resolution: 2→9.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.004→2.108 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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