+Open data
-Basic information
Entry | Database: PDB / ID: 3tpr | ||||||
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Title | Crystal structure of BACE1 complexed with an inhibitor | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / MEMAPSIN 2 / PROTEASE / Beta-secretase 1 / 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 / protein serine/threonine kinase binding / 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 / protein processing / recycling endosome / 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 / aspartic-type endopeptidase activity / lysosome / 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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Xu, Y.C. / Li, M.J. / Greenblatt, H. / Chen, T.T. / Silman, I. / Sussman, J.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations Authors: Xu, Y.C. / Li, M.J. / Greenblatt, H. / Chen, W.Y. / Paz, A. / Dym, O. / Peleg, Y. / Chen, T.T. / Shen, X. / He, J.H. / Jiang, H.L. / Silman, I. / Sussman, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tpr.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tpr.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 3tpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tpr_validation.pdf.gz | 811.8 KB | Display | wwPDB validaton report |
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Full document | 3tpr_full_validation.pdf.gz | 823 KB | Display | |
Data in XML | 3tpr_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3tpr_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/3tpr ftp://data.pdbj.org/pub/pdb/validation_reports/tp/3tpr | HTTPS FTP |
-Related structure data
Related structure data | 3tpjC 3tplC 3tppC 2b8lS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48339.059 Da / Num. of mol.: 1 / Fragment: UNP residues 43-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE, BACE1, KIAA1149 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 |
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#2: Chemical | ChemComp-5HA / |
#3: Chemical | ChemComp-CL / |
#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: 2.75 Å3/Da / Density % sol: 55.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20-25% (w/v) PEG 5000, monomethyl ether, 200mM ammonium iodide, 200mM sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 18527 / Observed criterion σ(I): 4.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B8L Resolution: 2.55→45.12 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.604 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.24 Å2 / Biso mean: 42.452 Å2 / Biso min: 13.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→45.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.547→2.613 Å / Total num. of bins used: 20
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