+Open data
-Basic information
Entry | Database: PDB / ID: 3uqr | ||||||
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Title | Crystal structure of BACE1 with its inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / 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 / 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 / amyloid fibril formation / aspartic-type endopeptidase activity / early endosome / lysosome / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.056 Å | ||||||
Authors | Chen, T.T. / Chen, W.Y. / Li, L. / Xu, Y.C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Cyanobacterial Peptides as a Prototype for the Design of Potent beta-Secretase Inhibitors and the Development of Selective Chemical Probes for Other Aspartic Proteases Authors: Liu, Y. / Zhang, W. / Li, L. / Salvador, L.A. / Chen, T.T. / Chen, W.Y. / Felsenstein, K.M. / Ladd, T.B. / Price, A.R. / Golde, T.E. / He, J. / Xu, Y.C. / Li, Y. / Luesch, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uqr.cif.gz | 238.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uqr.ent.gz | 188.5 KB | Display | PDB format |
PDBx/mmJSON format | 3uqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/3uqr ftp://data.pdbj.org/pub/pdb/validation_reports/uq/3uqr | HTTPS FTP |
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-Related structure data
Related structure data | 3uqpC 4dv9C 4dvfC 4fgxC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 48339.059 Da / Num. of mol.: 3 / Fragment: UNP residues 43-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 #2: Protein/peptide | Type: Polypeptide / Class: Enzyme inhibitor / Mass: 1024.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic peptide inhibitor / Source: (synth.) synthetic construct References: METHYL (2S)-1-[(2R,5S,8S,12S,13S)-2,13-DIBENZYL-12-HYDROXY-3,5-DIMETHYL-15-(3-[METHYL(METHYLSULFONYL)AMINO]-5-{[(1R)-1-PHENYLETHYL]CARBAMOYL}PHENYL)-8-(2-METHYLPROPYL)-4,7,10,15-TETRAOXO- ...References: METHYL (2S)-1-[(2R,5S,8S,12S,13S)-2,13-DIBENZYL-12-HYDROXY-3,5-DIMETHYL-15-(3-[METHYL(METHYLSULFONYL)AMINO]-5-{[(1R)-1-PHENYLETHYL]CARBAMOYL}PHENYL)-8-(2-METHYLPROPYL)-4,7,10,15-TETRAOXO-3,6,9,14-TETRAAZAPENTADECAN-1-OYL]PYRROLIDINE-2-CARBOXYLATE #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.26 % / Mosaicity: 0.19 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.0M Ammonium Sulfate, 0.1M Soldium Citrate, pH 5.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Mar 21, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.056→74.277 Å / Num. all: 43268 / Num. obs: 43268 / % possible obs: 96.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 51.41 Å2 / Rsym value: 0.094 / Net I/σ(I): 16.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B8L Resolution: 3.056→66.061 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8212 / SU ML: 0.36 / σ(F): 0 / Phase error: 24.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.543 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.03 Å2 / Biso mean: 57.3276 Å2 / Biso min: 19.53 Å2
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Refinement step | Cycle: LAST / Resolution: 3.056→66.061 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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