[English] 日本語
Yorodumi- PDB-2irz: Crystal structure of human Beta-secretase complexed with inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 2irz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human Beta-secretase complexed with inhibitor | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / Aspartyl Protease | ||||||
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 / detection of mechanical stimulus involved in sensory perception of pain / cellular response to manganese ion / 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 / detection of mechanical stimulus involved in sensory perception of pain / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / 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 / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / lysosome / early endosome / aspartic-type endopeptidase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Munshi, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Discovery of oxadiazoyl tertiary carbinamine inhibitors of beta-secretase (BACE-1). Authors: Rajapakse, H.A. / Nantermet, P.G. / Selnick, H.G. / Munshi, S. / McGaughey, G.B. / Lindsley, S.R. / Young, M.B. / Lai, M.T. / Espeseth, A.S. / Shi, X.P. / Colussi, D. / Pietrak, B. / ...Authors: Rajapakse, H.A. / Nantermet, P.G. / Selnick, H.G. / Munshi, S. / McGaughey, G.B. / Lindsley, S.R. / Young, M.B. / Lai, M.T. / Espeseth, A.S. / Shi, X.P. / Colussi, D. / Pietrak, B. / Crouthamel, M.C. / Tugusheva, K. / Huang, Q. / Xu, M. / Simon, A.J. / Kuo, L. / Hazuda, D.J. / Graham, S. / Vacca, J.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2irz.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2irz.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 2irz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2irz_validation.pdf.gz | 462.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2irz_full_validation.pdf.gz | 466.4 KB | Display | |
Data in XML | 2irz_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2irz_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/2irz ftp://data.pdbj.org/pub/pdb/validation_reports/ir/2irz | HTTPS FTP |
-Related structure data
Related structure data | 2is0C 1tqfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45122.750 Da / Num. of mol.: 1 / Fragment: protease domain / Mutation: K75A, E77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 |
---|---|
#2: Chemical | ChemComp-I02 / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.49 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.5M Lithium sulfate, 0.1M HEPES buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 45288 / Num. obs: 45288 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2 / Num. unique all: 4715 / % possible all: 96.8 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TQF Resolution: 1.8→6 Å / σ(F): 0 / σ(I): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
|