+Open data
-Basic information
Entry | Database: PDB / ID: 6nv7 | ||||||
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Title | BACE1 in complex with a macrocyclic inhibitor | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | PEPTIDE BINDING PROTEIN/Inhibitor / protease / inhibitor complex / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.132 Å | ||||||
Authors | Yen, Y.C. / Ghosh, A.K. / Mesecar, A.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Development of an Efficient Enzyme Production and Structure-Based Discovery Platform for BACE1 Inhibitors. Authors: Yen, Y.C. / Kammeyer, A.M. / Jensen, K.C. / Tirlangi, J. / Ghosh, A.K. / Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nv7.cif.gz | 247.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nv7.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 6nv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nv7_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6nv7_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6nv7_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 6nv7_validation.cif.gz | 68.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/6nv7 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/6nv7 | HTTPS FTP |
-Related structure data
Related structure data | 6nv9C 6nw3C 5dqcS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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-Components
#1: Protein | Mass: 43425.961 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) 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: 3.19 Å3/Da / Density % sol: 61.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgSO4 0.1 M sodium citrate 12-14 % PEG4000 / PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Aug 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→98 Å / Num. obs: 90383 / % possible obs: 99 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rpim(I) all: 0.035 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.13→2.21 Å / Mean I/σ(I) obs: 2.2 / CC1/2: 0.761 / Rpim(I) all: 0.344 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DQC Resolution: 2.132→55.465 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.132→55.465 Å
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Refine LS restraints |
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LS refinement shell |
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