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- PDB-3l59: Structure of BACE Bound to SCH710413 -

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Basic information

Entry
Database: PDB / ID: 3l59
TitleStructure of BACE Bound to SCH710413
ComponentsBeta-secretase 1
KeywordsHYDROLASE / BACE1 / Alzheimers / Alternative splicing / Aspartyl protease / Disulfide bond / Endoplasmic reticulum / Endosome / Glycoprotein / Golgi apparatus / Membrane / Polymorphism / Protease / Transmembrane / Zymogen
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 / amyloid-beta metabolic process / cellular response to manganese ion / 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 / amyloid-beta metabolic process / cellular response to manganese ion / 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 / multivesicular body / hippocampal mossy fiber to CA3 synapse / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / early endosome / lysosome / 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
Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BDJ / D(-)-TARTARIC ACID / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStrickland, C. / Zhu, Z.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Discovery of Cyclic Acylguanidines as Highly Potent and Selective beta-Site Amyloid Cleaving Enzyme (BACE) Inhibitors: Part I-Inhibitor Design and Validation
Authors: Zhu, Z. / Sun, Z.Y. / Ye, Y. / Voigt, J. / Strickland, C. / Smith, E.M. / Cumming, J. / Wang, L. / Wong, J. / Wang, Y.S. / Wyss, D.F. / Chen, X. / Kuvelkar, R. / Kennedy, M.E. / Favreau, L. ...Authors: Zhu, Z. / Sun, Z.Y. / Ye, Y. / Voigt, J. / Strickland, C. / Smith, E.M. / Cumming, J. / Wang, L. / Wong, J. / Wang, Y.S. / Wyss, D.F. / Chen, X. / Kuvelkar, R. / Kennedy, M.E. / Favreau, L. / Parker, E. / McKittrick, B.A. / Stamford, A. / Czarniecki, M. / Greenlee, W. / Hunter, J.C.
History
DepositionDec 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-secretase 1
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2026
Polymers92,5002
Non-polymers7024
Water15,295849
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6523
Polymers46,2501
Non-polymers4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5503
Polymers46,2501
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.304, 89.220, 131.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-secretase 1 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP cleaving enzyme 1 / Membrane- ...Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP cleaving enzyme 1 / Membrane-associated aspartic protease 2 / Memapsin-2 / Aspartyl protease 2 / Asp 2 / ASP2


Mass: 46249.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE, BACE1, KIAA1149 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-BDJ / (2Z)-3-(3-chlorobenzyl)-2-imino-5,5-dimethylimidazolidin-4-one


Mass: 251.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14ClN3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 277 K / Method: hanging drop / Details: Hanging Drop, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.22 Å / Num. obs: 68819 / % possible obs: 99.8 % / Rmerge(I) obs: 0.079 / Χ2: 1.061 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.070.32567850.85899.9
2.07-2.150.26467980.90299.9
2.15-2.250.21268110.92899.9
2.25-2.370.18568130.954100
2.37-2.520.16368400.9899.9
2.52-2.710.12668431.02999.8
2.71-2.990.09368951.097100
2.99-3.420.06569061.199100
3.42-4.310.04669711.399.8
4.31-500.03971571.25398.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.22 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.815 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.232 3474 5 %
Rwork0.205 --
obs-68735 99.6 %
Displacement parametersBiso max: 72.16 Å2 / Biso min: 7.46 Å2
Refinement stepCycle: LAST / Resolution: 2→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 47 849 7008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.389
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parasch710413.protopsch710413.pro
X-RAY DIFFRACTION2paratartrate.protoptartrate.pro
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.paramMSI_CNX_TOPPAR:water.top
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ion.paramMSI_CNX_TOPPAR:ion.top
X-RAY DIFFRACTION5MSI_CNX_TOPPAR:protein_rep.paramMSI_CNX_TOPPAR:protein.top

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