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Open data
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Basic information
Entry | Database: PDB / ID: 3udn | ||||||
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Title | Crystal Structure of BACE with Compound 9 | ||||||
![]() | Beta-secretase 1 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / multivesicular body / hippocampal mossy fiber to CA3 synapse / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / aspartic-type endopeptidase activity / amyloid fibril formation / endosome / endosome membrane / early endosome / lysosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / enzyme binding / cell surface / Golgi apparatus / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Efremov, I.V. / Vajdos, F.F. / Borzilleri, K. / Capetta, S. / Dorff, P. / Dutra, J. / Mansour, M. / Oborski, C. / O'Connell, T. / O'Sullivan, T.J. ...Efremov, I.V. / Vajdos, F.F. / Borzilleri, K. / Capetta, S. / Dorff, P. / Dutra, J. / Mansour, M. / Oborski, C. / O'Connell, T. / O'Sullivan, T.J. / Pandit, J. / Wang, H. / Withka, J. | ||||||
![]() | ![]() Title: Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design. Authors: Efremov, I.V. / Vajdos, F.F. / Borzilleri, K.A. / Capetta, S. / Chen, H. / Dorff, P.H. / Dutra, J.K. / Goldstein, S.W. / Mansour, M. / McColl, A. / Noell, S. / Oborski, C.E. / O'Connell, T.N. ...Authors: Efremov, I.V. / Vajdos, F.F. / Borzilleri, K.A. / Capetta, S. / Chen, H. / Dorff, P.H. / Dutra, J.K. / Goldstein, S.W. / Mansour, M. / McColl, A. / Noell, S. / Oborski, C.E. / O'Connell, T.N. / O'Sullivan, T.J. / Pandit, J. / Wang, H. / Wei, B. / Withka, J.M. #1: Journal: Protein Pept.Lett. / Year: 2008 Title: High yield expression of human BACE constructs in Escherichia coli for refolding, purification, and high resolution diffracting crystal forms. Authors: Tomasselli, A.G. / Paddock, D.J. / Emmons, T.L. / Mildner, A.M. / Leone, J.W. / Lull, J.M. / Cialdella, J.I. / Prince, D.B. / Fischer, H.D. / Heinrikson, R.L. / Benson, T.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 | ![]() | 94.2 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 705.6 KB | Display | ![]() |
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Full document | ![]() | 714.8 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3udhC ![]() 3udjC ![]() 3udkC ![]() 3udmC ![]() 3udpC ![]() 3udqC ![]() 3udrC ![]() 3udyC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45156.730 Da / Num. of mol.: 1 / Fragment: UNP residues 58-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 273 molecules ![](data/chem/img/09B.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-09B / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: protein in sodium borate, pH 8.5, reservoir: 30% PEG200, 0.1 M sodium acetate, pH 5.2-5.4, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 18, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.193→50 Å / Num. obs: 19236 / % possible obs: 97.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.103 / Χ2: 1.132 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: RIGID BODY REFINEMENT / Resolution: 2.193→24.75 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.411 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.282 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.99 Å2 / Biso mean: 29.7701 Å2 / Biso min: 11.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.193→24.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.193→2.249 Å / Total num. of bins used: 20
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