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- PDB-6ej2: BACE1 compound 28 -

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Basic information

Entry
Database: PDB / ID: 6ej2
TitleBACE1 compound 28
ComponentsBeta-secretase 1
KeywordsPEPTIDE BINDING PROTEIN / BACE1 / protease / Alzheimer
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
compound 28 / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsJohansson, P.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Toward beta-Secretase-1 Inhibitors with Improved Isoform Selectivity.
Authors: Johansson, P. / Kaspersson, K. / Gurrell, I.K. / Back, E. / Eketjall, S. / Scott, C.W. / Cebers, G. / Thorne, P. / McKenzie, M.J. / Beaton, H. / Davey, P. / Kolmodin, K. / Holenz, J. / ...Authors: Johansson, P. / Kaspersson, K. / Gurrell, I.K. / Back, E. / Eketjall, S. / Scott, C.W. / Cebers, G. / Thorne, P. / McKenzie, M.J. / Beaton, H. / Davey, P. / Kolmodin, K. / Holenz, J. / Duggan, M.E. / Budd Haeberlein, S. / Burli, R.W.
History
DepositionSep 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1942
Polymers55,8151
Non-polymers3781
Water4,648258
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.580, 101.580, 170.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1135-

HOH

21A-1241-

HOH

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Components

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


Mass: 55815.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-B7E / compound 28


Mass: 378.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 5k MME, 0.2M AmI, 0.2M sodium citrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.46→48.68 Å / Num. obs: 88595 / % possible obs: 97.9 % / Redundancy: 9 % / Biso Wilson estimate: 27.93 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 5.2
Reflection shellResolution: 1.46→1.51 Å / Rmerge(I) obs: 1.015

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→48.68 Å / Cor.coef. Fo:Fc: 0.9486 / Cor.coef. Fo:Fc free: 0.9421 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 3760 5.06 %RANDOM
Rwork0.2063 ---
obs0.2076 74343 82.21 %-
Displacement parametersBiso mean: 36.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.5186 Å20 Å20 Å2
2---1.5186 Å20 Å2
3---3.0372 Å2
Refine analyzeLuzzati coordinate error obs: 0.259 Å
Refinement stepCycle: 1 / Resolution: 1.46→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 28 258 3256
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083084HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024207HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1022SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes453HARMONIC5
X-RAY DIFFRACTIONt_it3084HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion17.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion398SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3664SEMIHARMONIC4
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2953 77 5.95 %
Rwork0.3038 1218 -
all0.3033 1295 -
obs--82.21 %
Refinement TLS params.Method: refined / Origin x: -15.0925 Å / Origin y: -40.917 Å / Origin z: 0.3879 Å
111213212223313233
T-0.0858 Å2-0.0172 Å2-0.0139 Å2--0.0305 Å20.0114 Å2---0.0437 Å2
L0.8541 °2-0.3313 °20.4245 °2-0.5653 °2-0.217 °2--0.9541 °2
S-0.0253 Å °-0.0164 Å °-0.0008 Å °0.0206 Å °0.0296 Å °0.0202 Å °-0.0119 Å °0.033 Å °-0.0044 Å °
Refinement TLS groupSelection details: { A|* }

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