+Open data
-Basic information
Entry | Database: PDB / ID: 5enm | ||||||
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Title | Compound 10 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / BACE / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.98 Å | ||||||
Authors | Lewis, H.A. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2016 Title: Targeting the BACE1 Active Site Flap Leads to a Potent Inhibitor That Elicits Robust Brain A beta Reduction in Rodents. Authors: Wu, Y.J. / Guernon, J. / Yang, F. / Snyder, L. / Shi, J. / Mcclure, A. / Rajamani, R. / Park, H. / Ng, A. / Lewis, H. / Chang, C. / Camac, D. / Toyn, J.H. / Ahlijanian, M.K. / Albright, C.F. ...Authors: Wu, Y.J. / Guernon, J. / Yang, F. / Snyder, L. / Shi, J. / Mcclure, A. / Rajamani, R. / Park, H. / Ng, A. / Lewis, H. / Chang, C. / Camac, D. / Toyn, J.H. / Ahlijanian, M.K. / Albright, C.F. / Macor, J.E. / Thompson, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5enm.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5enm.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 5enm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/5enm ftp://data.pdbj.org/pub/pdb/validation_reports/en/5enm | HTTPS FTP |
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-Related 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: 50220.492 Da / Num. of mol.: 1 / Fragment: UNP residues 14-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-IOD / |
#4: Chemical | ChemComp-5QU / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 10% PEG MME 5K, 9% PEG 8K, 0.2 M NH4I, 0.2 M Na-citrate pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→88.39 Å / Num. obs: 35629 / % possible obs: 100 % / Redundancy: 19 % / Net I/σ(I): 27.8 |
-Processing
Software |
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Refinement | Resolution: 1.98→88.39 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.823 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.341 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→88.39 Å
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Refine LS restraints |
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