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Yorodumi- PDB-2wf3: Human BACE-1 in complex with 6-(ethylamino)-N-((1S,2R)-2-hydroxy-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wf3 | ||||||
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Title | Human BACE-1 in complex with 6-(ethylamino)-N-((1S,2R)-2-hydroxy-3-(((3-(methyloxy)phenyl)methyl)amino)-1-(phenylmethyl)propyl)-1-methyl-1, 3,4,5-tetrahydro-2,1-benzothiazepine-8-carboxamide 2,2-dioxide | ||||||
Components | BETA-SECRETASE 1 | ||||||
Keywords | HYDROLASE / MEMAPSIN-2 / POLYMORPHISM / GLYCOPROTEIN / ASP-2 / BACE-1 / ZYMOGEN / PROTEASE / MEMBRANE / TRANSMEMBRANE / BETA-SECRETASE / DISULFIDE BOND / ASPARTYL PROTEASE / ALTERNATIVE SPLICING / BETA-SITE APP CLEAVING ENZYME | ||||||
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 / 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 / recycling endosome / protein processing / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.08 Å | ||||||
Authors | Charrier, N. / Clarke, B. / Demont, E. / Dingwall, C. / Dunsdon, R. / Hawkins, J. / Hubbard, J. / Hussain, I. / Maile, G. / Matico, R. ...Charrier, N. / Clarke, B. / Demont, E. / Dingwall, C. / Dunsdon, R. / Hawkins, J. / Hubbard, J. / Hussain, I. / Maile, G. / Matico, R. / Mosley, J. / Naylor, A. / O'Brien, A. / Redshaw, S. / Rowland, P. / Soleil, V. / Smith, K.J. / Sweitzer, S. / Theobald, P. / Vesey, D. / Walter, D.S. / Wayne, G. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Second Generation of Bace-1 Inhibitors Part 2: Optimisation of the Non-Prime Side Substituent. Authors: Charrier, N. / Clarke, B. / Demont, E. / Dingwall, C. / Dunsdon, R. / Hawkins, J. / Hubbard, J. / Hussain, I. / Maile, G. / Matico, R. / Mosley, J. / Naylor, A. / O'Brien, A. / Redshaw, S. / ...Authors: Charrier, N. / Clarke, B. / Demont, E. / Dingwall, C. / Dunsdon, R. / Hawkins, J. / Hubbard, J. / Hussain, I. / Maile, G. / Matico, R. / Mosley, J. / Naylor, A. / O'Brien, A. / Redshaw, S. / Rowland, P. / Soleil, V. / Smith, K.J. / Sweitzer, S. / Theobald, P. / Vesey, D. / Walter, D.S. / Wayne, G. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wf3.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wf3.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wf3_validation.pdf.gz | 768.7 KB | Display | wwPDB validaton report |
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Full document | 2wf3_full_validation.pdf.gz | 773 KB | Display | |
Data in XML | 2wf3_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 2wf3_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wf3 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wf3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43761.312 Da / Num. of mol.: 1 / Fragment: RESIDUES 61-452 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P56817, memapsin 2 | ||||
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#2: Chemical | ChemComp-ZY3 / | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN ...ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.33 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: CRYSTALS GROWN BY VAPOUR DIFFUSION AT 20C USING STREAK SEEDING, WITH 10% PEG8000 AND 0.1M GLYCINE PH 3.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→40 Å / Num. obs: 24009 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.08→2.12 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.6 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.08→61.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 17.97 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→61.9 Å
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LS refinement shell | Resolution: 2.081→2.135 Å / Total num. of bins used: 20
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