+Open data
-Basic information
Entry | Database: PDB / ID: 6qb4 | ||||||
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Title | Mcl1-scFv complex with an indole acid inhibitor | ||||||
Components |
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Keywords | APOPTOSIS / Mcl1 / scFv / indole acid | ||||||
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 / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity ...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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | 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 | 6qb4.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qb4.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 6qb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qb4_validation.pdf.gz | 559.5 KB | Display | wwPDB validaton report |
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Full document | 6qb4_full_validation.pdf.gz | 560.9 KB | Display | |
Data in XML | 6qb4_validation.xml.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/6qb4 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/6qb4 | HTTPS FTP |
-Related structure data
Related structure data | 6qb3C 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: Chemical | ChemComp-HVN / |
#4: 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: 2.39 Å3/Da / Density % sol: 48.49 % |
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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: I04-1 / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→42.15 Å / Num. obs: 16889 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 37.27 Å2 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.38→2.51 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→39.11 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.399 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.235
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Displacement parameters | Biso mean: 36.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.38→39.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.4 Å / Total num. of bins used: 43
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