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- PDB-2ewy: Crystal structure of human BACE2 in complex with a hydroxyethylen... -

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Basic information

Entry
Database: PDB / ID: 2ewy
TitleCrystal structure of human BACE2 in complex with a hydroxyethylenamine transition-state inhibitor
ComponentsBeta-secretase 2
KeywordsHYDROLASE / BACE2 / aspartic protease
Function / homology
Function and homology information


memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis ...memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / Golgi apparatus / endoplasmic reticulum / proteolysis / membrane / plasma membrane
Similarity search - Function
Beta-secretase BACE2 / 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 BACE2 / 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-DBO / Beta-secretase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsOstermann, N.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of human BACE2 in complex with a hydroxyethylamine transition state inhibitor
Authors: Ostermann, N. / Eder, J. / Eidhoff, U. / Zink, F. / Hassiepen, U. / Worpenberg, S. / Maibaum, J. / Simic, O. / Hommel, U. / Gerhartz, B.
History
DepositionNov 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 2
B: Beta-secretase 2
C: Beta-secretase 2
D: Beta-secretase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,1118
Polymers167,0924
Non-polymers2,0184
Water2,414134
1
A: Beta-secretase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2782
Polymers41,7731
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Beta-secretase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2782
Polymers41,7731
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Beta-secretase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2782
Polymers41,7731
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Beta-secretase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2782
Polymers41,7731
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
A: Beta-secretase 2
B: Beta-secretase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5554
Polymers83,5462
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-34 kcal/mol
Surface area29080 Å2
MethodPISA
6
C: Beta-secretase 2
D: Beta-secretase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5554
Polymers83,5462
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-34 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.407, 228.407, 108.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.30485, 0.9524, -0.0022), (0.9524, -0.30484, 0.00064), (-6.0E-5, -0.00229, -1)52.63405, -72.33963, -37.90527
3given(0.5112, 0.85946, -0.00251), (-0.85946, 0.51119, -0.00234), (-0.00072, 0.00335, 0.99999)37.14735, 64.74499, 18.10184
4given(0.97976, 0.1998, -0.01239), (0.19995, -0.97972, 0.01268), (-0.00961, -0.0149, -0.99984)1.85155, -14.51931, -18.56605
DetailsThe biological assembly is a monomer.

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Components

#1: Protein
Beta-secretase 2 / / Beta-site APP-cleaving enzyme 2 / Aspartyl protease 1 / Asp 1 / ASP1 / Membrane-associated aspartic ...Beta-site APP-cleaving enzyme 2 / Aspartyl protease 1 / Asp 1 / ASP1 / Membrane-associated aspartic protease 1 / Memapsin-1 / Down region aspartic protease


Mass: 41773.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE2, ASP21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5Z0, memapsin 1
#2: Chemical
ChemComp-DBO / N-{(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHYLBENZYL)AMINO]PROPYL}DIBENZO[B,F]OXEPINE-10-CARBOXAMIDE


Mass: 504.619 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H32N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 16% PEG 8000, 0.1M calcium chloride, 5% glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97935 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.05→25.5 Å / Num. obs: 39813 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 64.2 Å2
Reflection shellResolution: 3.05→3.16 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNX2000.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FKN

1fkn


Resolution: 3.1→24.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3297744.17 / Data cutoff high rms absF: 3297744.17 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3795 10 %RANDOM
Rwork0.227 ---
all-39813 --
obs-38029 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.202085 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.07 Å2-4.66 Å20 Å2
2---8.07 Å20 Å2
3---16.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-25 Å
Luzzati sigma a0.38 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 3.1→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11572 0 152 134 11858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 612 9.6 %
Rwork0.326 5735 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3inh.parinh.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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