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- PDB-2ohn: X-ray crystal structure of beta secretase complexed with 4-(4-flu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ohn | ||||||
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Title | X-ray crystal structure of beta secretase complexed with 4-(4-fluorobenzyl)piperidine | ||||||
![]() | Beta-secretase 1 | ||||||
![]() | HYDROLASE / ALTERNATIVE SPLICING / ALZHEIMER'S DISEASE / ASPARTIC PROTEASE / ASPARTYL PROTEASE / BASE / BETA-SECRETASE / GLYCOPROTEIN / MEMAPSIN 2 / TRANSMEMBRANE / ZYMOGEN | ||||||
Function / homology | ![]() 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 / hippocampal mossy fiber to CA3 synapse / 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 / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / lysosome / early endosome / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patel, S. | ||||||
![]() | ![]() Title: Application of fragment screening by X-ray crystallography to beta-Secretase. Authors: Murray, C.W. / Callaghan, O. / Chessari, G. / Cleasby, A. / Congreve, M. / Frederickson, M. / Hartshorn, M.J. / McMenamin, R. / Patel, S. / Wallis, N. | ||||||
History |
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Remark 600 | HETEROGEN THERE IS AN EXTRA ATOM H12 IN MOLECULE 4FP. AUTHOR STATES THAT THE MOLECULE 4FP IS ... HETEROGEN THERE IS AN EXTRA ATOM H12 IN MOLECULE 4FP. AUTHOR STATES THAT THE MOLECULE 4FP IS PROTONATED (CHARGED) UNDER THE PH CONDITIONS OF THE EXPERIMENT, AND THIS PROTONATION STATE IS CRITICAL TO THE BINDING MODE OBSERVED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.9 KB | Display | ![]() |
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PDB format | ![]() | 72.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.5 KB | Display | ![]() |
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Full document | ![]() | 466.2 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2of0C ![]() 2ohkC ![]() 2ohlC ![]() 2ohmC ![]() 1w50S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 44841.395 Da / Num. of mol.: 1 / Fragment: protease domain / Mutation: R56K, R57K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-4FP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 20-22.5% (w/v) PEG 5000 monomethylether (MME), 200 mM sodium citrate (pH 6.6), 200 mM ammonium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→47.79 Å / Num. all: 29243 / Num. obs: 29243 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1W50 Resolution: 2.15→47.79 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.677 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.333 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→47.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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