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Yorodumi- PDB-2fdp: Crystal structure of beta-secretase complexed with an amino-ethyl... -
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-Basic information
Entry | Database: PDB / ID: 2fdp | ||||||
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Title | Crystal structure of beta-secretase complexed with an amino-ethylene inhibitor | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / ASPARTYL PROTEASE / BACE | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Yang, W. / Lu, W. / Lu, Y. / Zhong, M. / Sun, J. / Thomas, A.E. / Wilkinson, J.M. / Fucini, R.V. / Lam, M. / Randal, M. ...Yang, W. / Lu, W. / Lu, Y. / Zhong, M. / Sun, J. / Thomas, A.E. / Wilkinson, J.M. / Fucini, R.V. / Lam, M. / Randal, M. / Shi, X.P. / Jacobs, J.W. / McDowell, R.S. / Gordon, E.M. / Ballinger, M.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Aminoethylenes: a tetrahedral intermediate isostere yielding potent inhibitors of the aspartyl protease BACE-1. Authors: Yang, W. / Lu, W. / Lu, Y. / Zhong, M. / Sun, J. / Thomas, A.E. / Wilkinson, J.M. / Fucini, R.V. / Lam, M. / Randal, M. / Shi, X.P. / Jacobs, J.W. / McDowell, R.S. / Gordon, E.M. / Ballinger, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fdp.cif.gz | 227.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fdp.ent.gz | 183.2 KB | Display | PDB format |
PDBx/mmJSON format | 2fdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/2fdp ftp://data.pdbj.org/pub/pdb/validation_reports/fd/2fdp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 43255.754 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P56817, memapsin 2 #2: Chemical | #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: 3.1 Å3/Da / Density % sol: 60.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.79 Å / Num. all: 54657 / Num. obs: 54657 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5423 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: previously refined model Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.434 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.441 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 21.082 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.586 Å / Total num. of bins used: 15
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