+Open data
-Basic information
Entry | Database: PDB / ID: 6qb3 | ||||||
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Title | Apo Mcl1 in a complex with a scFv | ||||||
Components |
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Keywords | APOPTOSIS / Mcl1-scFv complex | ||||||
Function / homology | Function and homology information positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / mitochondrial fusion / channel activity / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / mitochondrial fusion / channel activity / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / Signaling by ALK fusions and activated point mutants / intrinsic apoptotic signaling pathway in response to DNA damage / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kazmirski, S. / Hargreaves, D. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Antibody fragments structurally enable a drug-discovery campaign on the cancer target Mcl-1. Authors: Luptak, J. / Bista, M. / Fisher, D. / Flavell, L. / Gao, N. / Wickson, K. / Kazmirski, S.L. / Howard, T. / Rawlins, P.B. / Hargreaves, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qb3.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qb3.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/6qb3 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/6qb3 | HTTPS FTP |
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-Related structure data
Related structure data | 6qb4C 6qb6C 6qb9C 6qbcC 6qf9C 6qfcC C: citing same article (ref.) |
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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: 18227.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820 |
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#2: Antibody | Mass: 26428.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
#3: 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: 2.28 Å3/Da / Density % sol: 46.17 % Description: multiple long thin plates growing from a central nucleation site |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PCPT 0.1M pH 7.5, PEG 3350 15%w/v, MgCl2 0.1M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.85 Å / Num. obs: 32161 / % possible obs: 99.4 % / Redundancy: 2 % / Biso Wilson estimate: 23.38 Å2 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.9→2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.66 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.124
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Displacement parameters | Biso mean: 37.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→38.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å / Total num. of bins used: 50
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