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Yorodumi- PDB-2vj7: Human BACE-1 in complex with 3-(ethylamino)-N-((1S,2R)-2-hydroxy-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vj7 | ||||||
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Title | Human BACE-1 in complex with 3-(ethylamino)-N-((1S,2R)-2-hydroxy-1-(phenylmethyl)-3-(((3-(trifluoromethyl)phenyl)methyl)amino)propyl)-5-(2-oxo-1-pyrrolidinyl)benzamide | ||||||
Components | BETA-SECRETASE 1 | ||||||
Keywords | HYDROLASE / ALTERNATIVE SPLICING / BETA-SITE APP CLEAVING ENZYME / BETA-SECRETASE / ASPARTYL PROTEASE / ASP-2 / BACE-1 / ZYMOGEN / PROTEASE / MEMBRANE / MEMAPSIN-2 / GLYCOPROTEIN / TRANSMEMBRANE | ||||||
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 / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.6 Å | ||||||
Authors | Clarke, B. / Demont, E. / Dingwall, C. / Dunsdon, R. / Faller, A. / Hawkins, J. / Hussain, I. / MacPherson, D. / Maile, G. / Matico, R. ...Clarke, B. / Demont, E. / Dingwall, C. / Dunsdon, R. / Faller, A. / Hawkins, J. / Hussain, I. / MacPherson, D. / Maile, G. / Matico, R. / Milner, P. / Mosley, J. / Naylor, A. / O'Brien, A. / Redshaw, S. / Riddell, D. / Rowland, P. / Soleil, V. / Smith, K. / Stanway, S. / Stemp, G. / Sweitzer, S. / Theobald, P. / Vesey, D. / Walter, D.S. / Ward, J. / Wayne, G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Bace-1 Inhibitors Part 2: Identification of Hydroxy Ethylamines (Heas) with Reduced Peptidic Character. Authors: Clarke, B. / Demont, E. / Dingwall, C. / Dunsdon, R. / Faller, A. / Hawkins, J. / Hussain, I. / Macpherson, D. / Maile, G. / Matico, R. / Milner, P. / Mosley, J. / Naylor, A. / O'Brien, A. / ...Authors: Clarke, B. / Demont, E. / Dingwall, C. / Dunsdon, R. / Faller, A. / Hawkins, J. / Hussain, I. / Macpherson, D. / Maile, G. / Matico, R. / Milner, P. / Mosley, J. / Naylor, A. / O'Brien, A. / Redshaw, S. / Riddell, D. / Rowland, P. / Soleil, V. / Smith, K. / Stanway, S. / Stemp, G. / Sweitzer, S. / Theobald, P. / Vesey, D. / Walter, D.S. / Ward, J. / Wayne, G. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vj7.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vj7.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vj7_validation.pdf.gz | 781.6 KB | Display | wwPDB validaton report |
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Full document | 2vj7_full_validation.pdf.gz | 787.1 KB | Display | |
Data in XML | 2vj7_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 2vj7_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vj7 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vj7 | HTTPS FTP |
-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: 43761.312 Da / Num. of mol.: 1 / Fragment: RESIDUES 61-452 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY / References: UniProt: P56817, memapsin 2 |
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#2: Chemical | ChemComp-VG6 / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.03 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: CRYSTALS GROWN BY VAPOUR DIFFUSION AT 20C USING STREAK SEEDING, WITH 10% PEG8000 AND 0.1M GLYCINE PH 3.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. obs: 48870 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.6 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.6→25 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.63 Å / Rfactor Rfree: 0.304 / Rfactor Rwork: 0.255 / Rfactor Rfree error: 0.045 / Total num. of bins used: 39 |