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- PDB-3cid: Structure of BACE Bound to SCH726222 -

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Basic information

Entry
Database: PDB / ID: 3cid
TitleStructure of BACE Bound to SCH726222
ComponentsBeta-secretase 1
KeywordsHYDROLASE / BACE1 / 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 / cellular response to manganese ion / prepulse inhibition / 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 / cellular response to manganese ion / prepulse inhibition / amyloid-beta metabolic process / detection of mechanical stimulus involved in sensory perception of pain / cellular response to copper ion / hippocampal mossy fiber to CA3 synapse / presynaptic modulation of chemical synaptic transmission / 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 / amyloid-beta binding / peptidase activity / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / 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-318 / D(-)-TARTARIC ACID / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsStrickland, C. / Cumming, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors
Authors: Cumming, J.N. / Le, T.X. / Babu, S. / Carroll, C. / Chen, X. / Favreau, L. / Gaspari, P. / Guo, T. / Hobbs, D.W. / Huang, Y. / Iserloh, U. / Kennedy, M.E. / Kuvelkar, R. / Li, G. / Lowrie, J. ...Authors: Cumming, J.N. / Le, T.X. / Babu, S. / Carroll, C. / Chen, X. / Favreau, L. / Gaspari, P. / Guo, T. / Hobbs, D.W. / Huang, Y. / Iserloh, U. / Kennedy, M.E. / Kuvelkar, R. / Li, G. / Lowrie, J. / McHugh, N.A. / Ozgur, L. / Pan, J. / Parker, E.M. / Saionz, K. / Stamford, A.W. / Strickland, C. / Tadesse, D. / Voigt, J. / Wang, L. / Wu, Y. / Zhang, L. / Zhang, Q.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,5167
Polymers86,8522
Non-polymers1,6645
Water17,168953
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1833
Polymers43,4261
Non-polymers7572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3334
Polymers43,4261
Non-polymers9073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.296, 89.131, 130.590
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 / / E.C.3.4.23.46 / Beta-site APP cleaving enzyme 1 / Beta-site amyloid precursor protein cleaving enzyme 1 / Membrane- ...Beta-site APP cleaving enzyme 1 / Beta-site amyloid precursor protein cleaving enzyme 1 / Membrane-associated aspartic protease 2 / Memapsin-2 / Aspartyl protease 2 / Asp 2 / ASP2


Mass: 43425.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-318 / N'-[(1S,2S)-2-[(4S)-1-benzyl-5-oxoimidazolidin-4-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide


Mass: 606.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H40F2N4O4
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 953 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 95484 / Num. obs: 95380 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Χ2: 1.06 / Net I/σ(I): 25.3
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4732 / Rsym value: 0.489 / Χ2: 1.005 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CNSphasing
RefinementResolution: 1.8→50 Å / FOM work R set: 0.841 / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.221 4709 5 %
Rwork0.194 --
all-95484 -
obs-93720 99.9 %
Displacement parametersBiso mean: 23.062 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 88 983 7183
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.756
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parasch726222.protopsch726222.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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