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Yorodumi- PDB-1m4h: Crystal Structure of Beta-secretase complexed with Inhibitor OM00-3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m4h | |||||||||
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Title | Crystal Structure of Beta-secretase complexed with Inhibitor OM00-3 | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / MEMAPSIN2 / BASE / ASP2 / ALZHEIMER'S DISEASE / ASPARTIC PROTEASE / ACID PROTEASE / 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 / prepulse inhibition / amyloid-beta metabolic process ...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 / prepulse inhibition / amyloid-beta metabolic process / detection of mechanical stimulus involved in sensory perception of pain / cellular response to copper ion / hippocampal mossy fiber to CA3 synapse / presynaptic modulation of chemical synaptic transmission / 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 / amyloid-beta binding / peptidase activity / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Hong, L. / Turner, R.T. / Koelsch, G. / Ghosh, A.K. / Tang, J. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal Structure of Memapsin 2 (beta-Secretase) in Complex with Inhibitor OM00-3 Authors: Hong, L. / Turner, R.T. / Koelsch, G. / Shin, D. / Ghosh, A.K. / Tang, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m4h.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m4h.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/1m4h ftp://data.pdbj.org/pub/pdb/validation_reports/m4/1m4h | HTTPS FTP |
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-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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Unit cell |
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-Components
#1: Protein | Mass: 43627.191 Da / Num. of mol.: 2 / Fragment: Protease Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE / Production host: Escherichia coli (E. coli) References: UniProt: P56817, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases #2: Protein/peptide | #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: 2.82 Å3/Da / Density % sol: 56.37 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22.5% PEG 8000, 0.2 M Ammonium Sulfate, 0.1 M Sodium Cacodylate, pH 6.2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.2 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 2001 / Details: mirrors |
Radiation | Monochromator: multilayer reflector / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 59470 / Num. obs: 58812 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.2 / % possible all: 97.1 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 58864 / % possible obs: 98.8 % / Num. measured all: 190727 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 97.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1FKN Resolution: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.1 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011
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Refine LS restraints | *PLUS
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