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- PDB-5dqc: Co-crystal of BACE1 with compound 0211 -

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Basic information

Entry
Database: PDB / ID: 5dqc
TitleCo-crystal of BACE1 with compound 0211
ComponentsBeta-secretase 1
KeywordsHydrolase/Hydrolase Inhibitor / B-secretase / inhibitor / Alzheimer's disease / Hydrolase-Hydrolase 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 / amyloid-beta metabolic process / cellular response to manganese ion ...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 / amyloid-beta metabolic process / cellular response to manganese ion / 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 / aspartic-type endopeptidase activity / 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
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-5E7 / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4651 Å
AuthorsGhosh, A.K. / Bhavanam, S.R. / Yen, T.-C. / Cardenas, E.L. / Rao, K.V. / Downs, D. / Huang, X. / Tang, J. / Mescar, A.D.
CitationJournal: Chem Sci / Year: 2016
Title: Design of Potent and Highly Selective Inhibitors for Human beta-Secretase 2 (Memapsin 1), a Target for Type 2 Diabetes.
Authors: Ghosh, A.K. / Reddy, B.S. / Yen, Y.C. / Cardenas, E. / Rao, K.V. / Downs, D. / Huang, X. / Tang, J. / Mesecar, A.D.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references

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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
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3656
Polymers130,2783
Non-polymers2,0883
Water2,306128
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1222
Polymers43,4261
Non-polymers6961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1222
Polymers43,4261
Non-polymers6961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1222
Polymers43,4261
Non-polymers6961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.950, 103.403, 100.834
Angle α, β, γ (deg.)90.000, 102.660, 90.000
Int Tables number4
Space group name H-MP1211

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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: 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 (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-5E7 / N-[(2S,3R)-3-hydroxy-4-({(2S,3S)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide


Mass: 695.869 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H49N5O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400 Na citrate MgSO4 / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.46→100 Å / Num. obs: 58492 / % possible obs: 90.6 % / Redundancy: 3.4 % / Net I/σ(I): 26.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.4651→45.767 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 1999 3.78 %
Rwork0.1847 50945 -
obs0.1867 52944 89.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.31 Å2 / Biso mean: 60.0407 Å2 / Biso min: 31.86 Å2
Refinement stepCycle: final / Resolution: 2.4651→45.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8781 0 147 128 9056
Biso mean--50.88 53.99 -
Num. residues----1114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059165
X-RAY DIFFRACTIONf_angle_d0.96312442
X-RAY DIFFRACTIONf_chiral_restr0.0341345
X-RAY DIFFRACTIONf_plane_restr0.0041596
X-RAY DIFFRACTIONf_dihedral_angle_d15.6113254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4651-2.52680.31731090.27652768X-RAY DIFFRACTION68
2.5268-2.59510.33911340.26343438X-RAY DIFFRACTION85
2.5951-2.67140.31511340.26983422X-RAY DIFFRACTION85
2.6714-2.75760.35181370.25033469X-RAY DIFFRACTION85
2.7576-2.85620.30081360.24673463X-RAY DIFFRACTION85
2.8562-2.97050.31731370.22743518X-RAY DIFFRACTION87
2.9705-3.10570.27681410.21813583X-RAY DIFFRACTION88
3.1057-3.26940.2741430.21323641X-RAY DIFFRACTION89
3.2694-3.47420.25851450.20123700X-RAY DIFFRACTION91
3.4742-3.74230.22911510.18723863X-RAY DIFFRACTION95
3.7423-4.11870.21111560.16643964X-RAY DIFFRACTION97
4.1187-4.71410.21451560.15143995X-RAY DIFFRACTION98
4.7141-5.93730.21191600.16574067X-RAY DIFFRACTION99
5.9373-100.19061600.16344054X-RAY DIFFRACTION97

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