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Yorodumi- PDB-2g94: Crystal structure of beta-secretase bound to a potent and highly ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g94 | ||||||
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Title | Crystal structure of beta-secretase bound to a potent and highly selective inhibitor. | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / beta secretase / Alzheimer's disease / memapsin / BACE / ASP2 / Aspartic protease / drug design / protease inhibitor | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Hong, L. / Ghosh, A. / Tang, J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2006 Title: Design, synthesis and X-ray structure of protein-ligand complexes: important insight into selectivity of memapsin 2 (beta-secretase) inhibitors. Authors: Ghosh, A.K. / Kumaragurubaran, N. / Hong, L. / Lei, H. / Hussain, K.A. / Liu, C.F. / Devasamudram, T. / Weerasena, V. / Turner, R. / Koelsch, G. / Bilcer, G. / Tang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g94.cif.gz | 328.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g94.ent.gz | 266.5 KB | Display | PDB format |
PDBx/mmJSON format | 2g94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g94_validation.pdf.gz | 683.2 KB | Display | wwPDB validaton report |
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Full document | 2g94_full_validation.pdf.gz | 705.7 KB | Display | |
Data in XML | 2g94_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 2g94_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/2g94 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/2g94 | HTTPS FTP |
-Related structure data
Related structure data | 1fknS 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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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 43312.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P56817, memapsin 2 #2: Chemical | ChemComp-ZPQ / #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: 2.87 Å3/Da / Density % sol: 57.07 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Apo enzyme crystal was obtained at 15% PEG 8000, PH 6.5 in Sodium Cacodylate buffer. The apo enzyme crystal was soaked in concentrated inhibitor solution to make the enzyme/inhibitor complex ...Details: Apo enzyme crystal was obtained at 15% PEG 8000, PH 6.5 in Sodium Cacodylate buffer. The apo enzyme crystal was soaked in concentrated inhibitor solution to make the enzyme/inhibitor complex crystal for X-ray data collection, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 19, 2003 |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→46.38 Å / Num. all: 163375 / Num. obs: 161086 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.86→1.93 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.4 / Num. unique all: 15349 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1fkn Resolution: 1.86→46.38 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.86→46.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.98 Å / Rfactor Rfree error: 0.007
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