+Open data
-Basic information
Entry | Database: PDB / ID: 6nco | ||||||
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Title | Fragment-based Discovery of an apoE4 Stabilizer | ||||||
Components | Apolipoprotein E | ||||||
Keywords | LIPID TRANSPORT / Lipid Binding | ||||||
Function / homology | Function and homology information chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle ...chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle / regulation of amyloid-beta clearance / discoidal high-density lipoprotein particle / intermediate-density lipoprotein particle / chylomicron remnant clearance / maintenance of location in cell / very-low-density lipoprotein particle clearance / very-low-density lipoprotein particle remodeling / Chylomicron clearance / negative regulation of triglyceride metabolic process / response to caloric restriction / acylglycerol homeostasis / NMDA glutamate receptor clustering / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / regulation of amyloid fibril formation / regulation of protein metabolic process / high-density lipoprotein particle clearance / multivesicular body, internal vesicle / lipoprotein catabolic process / melanosome organization / lipid transporter activity / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / phospholipid efflux / AMPA glutamate receptor clustering / cholesterol transfer activity / positive regulation by host of viral process / reverse cholesterol transport / very-low-density lipoprotein particle / positive regulation of amyloid-beta clearance / high-density lipoprotein particle assembly / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / protein import / negative regulation of blood coagulation / high-density lipoprotein particle / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / heparan sulfate proteoglycan binding / synaptic transmission, cholinergic / negative regulation of cholesterol biosynthetic process / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / amyloid precursor protein metabolic process / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / negative regulation of blood vessel endothelial cell migration / negative regulation of protein metabolic process / HDL remodeling / negative regulation of endothelial cell migration / Scavenging by Class A Receptors / artery morphogenesis / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / positive regulation of cholesterol efflux / triglyceride metabolic process / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / positive regulation of dendritic spine development / regulation of innate immune response / virion assembly / long-chain fatty acid transport / locomotory exploration behavior / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / regulation of neuronal synaptic plasticity / positive regulation of endocytosis / lipoprotein particle binding / antioxidant activity / response to dietary excess / negative regulation of long-term synaptic potentiation / positive regulation of dendritic spine maintenance / negative regulation of platelet activation / intracellular transport / regulation of protein-containing complex assembly / negative regulation of protein secretion / fatty acid homeostasis / cholesterol catabolic process / long-term memory / positive regulation of lipid biosynthetic process / regulation of proteasomal protein catabolic process / synaptic cleft Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.707 Å | ||||||
Authors | Jakob, C.G. / Qiu, W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Fragment-Based Discovery of an Apolipoprotein E4 (apoE4) Stabilizer. Authors: Petros, A.M. / Korepanova, A. / Jakob, C.G. / Qiu, W. / Panchal, S.C. / Wang, J. / Dietrich, J.D. / Brewer, J.T. / Pohlki, F. / Kling, A. / Wilcox, K. / Lakics, V. / Bahnassawy, L. / ...Authors: Petros, A.M. / Korepanova, A. / Jakob, C.G. / Qiu, W. / Panchal, S.C. / Wang, J. / Dietrich, J.D. / Brewer, J.T. / Pohlki, F. / Kling, A. / Wilcox, K. / Lakics, V. / Bahnassawy, L. / Reinhardt, P. / Partha, S.K. / Bodelle, P.M. / Lake, M. / Charych, E.I. / Stoll, V.S. / Sun, C. / Mohler, E.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nco.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nco.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 6nco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nco_validation.pdf.gz | 770.4 KB | Display | wwPDB validaton report |
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Full document | 6nco_full_validation.pdf.gz | 771.3 KB | Display | |
Data in XML | 6nco_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 6nco_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/6nco ftp://data.pdbj.org/pub/pdb/validation_reports/nc/6nco | HTTPS FTP |
-Related structure data
Related structure data | 6ncnC 1gs9S S: Starting model for refinement 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: 21523.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOE / Production host: Escherichia coli (E. coli) / References: UniProt: P02649 |
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#2: Chemical | ChemComp-KQP / |
#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: 2.17 Å3/Da / Density % sol: 43.43 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 20% w/v Polyethylene glycol monomethyl ether mesylate 5,000; 0.1M Bis-Tris buffer at pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.707→45.105 Å / Num. obs: 20917 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.707→1.737 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 972 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GS9 Resolution: 1.707→33.462 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.707→33.462 Å
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Refine LS restraints |
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LS refinement shell |
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