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- PDB-2wez: Human BACE-1 in complex with 1-ethyl-N-((1S,2R)-2-hydroxy-3-(((3-... -

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Basic information

Entry
Database: PDB / ID: 2wez
TitleHuman BACE-1 in complex with 1-ethyl-N-((1S,2R)-2-hydroxy-3-(((3-(methyloxy)phenyl)methyl)amino)-1-(phenylmethyl)propyl)-4-(2-oxo-1- pyrrolidinyl)-1H-indole-6-carboxamide
ComponentsBETA-SECRETASE 1
KeywordsHYDROLASE / MEMAPSIN-2 / POLYMORPHISM / GLYCOPROTEIN / ASP-2 / BACE-1 / ZYMOGEN / PROTEASE / MEMBRANE / TRANSMEMBRANE / BETA-SECRETASE / DISULFIDE BOND / ASPARTYL PROTEASE / ALTERNATIVE SPLICING / BETA-SITE APP CLEAVING ENZYME
Function / homology
Function and homology information


memapsin 2 / Golgi-associated vesicle lumen / beta-aspartyl-peptidase activity / signaling receptor ligand precursor processing / 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 / beta-aspartyl-peptidase activity / signaling receptor ligand precursor processing / 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 / cellular response to copper ion / protein serine/threonine kinase binding / presynaptic modulation of chemical synaptic transmission / multivesicular body / hippocampal mossy fiber to CA3 synapse / trans-Golgi network / response to lead ion / protein processing / recycling endosome / 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 / endosome membrane / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / enzyme binding / cell surface / Golgi apparatus / 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-ZYE / Beta-secretase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsCharrier, N. / Clarke, B. / Cutler, L. / Demont, E. / Dingwall, C. / Dunsdon, R. / Hawkins, J. / Howes, C. / Hubbard, J. / Hussain, I. ...Charrier, N. / Clarke, B. / Cutler, L. / Demont, E. / Dingwall, C. / Dunsdon, R. / Hawkins, J. / Howes, C. / Hubbard, J. / Hussain, I. / Maile, G. / Matico, R. / Mosley, J. / Naylor, A. / O'Brien, A. / Redshaw, S. / Rowland, P. / Soleil, V. / Smith, K.J. / Sweitzer, S. / Theobald, P. / Vesey, D. / Walter, D.S. / Wayne, G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Second Generation of Bace-1 Inhibitors. Part 1: The Need for Improved Pharmacokinetics.
Authors: Charrier, N. / Clarke, B. / Cutler, L. / Demont, E. / Dingwall, C. / Dunsdon, R. / Hawkins, J. / Howes, C. / Hubbard, J. / Hussain, I. / Maile, G. / Matico, R. / Mosley, J. / Naylor, A. / ...Authors: Charrier, N. / Clarke, B. / Cutler, L. / Demont, E. / Dingwall, C. / Dunsdon, R. / Hawkins, J. / Howes, C. / Hubbard, J. / Hussain, I. / Maile, G. / Matico, R. / Mosley, J. / Naylor, A. / O'Brien, A. / Redshaw, S. / Rowland, P. / Soleil, V. / Smith, K.J. / Sweitzer, S. / Theobald, P. / Vesey, D. / Walter, D.S. / Wayne, G.
History
DepositionApr 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-SECRETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3162
Polymers43,7611
Non-polymers5551
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.531, 76.758, 104.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2 / ...BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1 / MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2 / MEMAPSIN-2 / ASPARTYL PROTEASE 2 / BETA-SITE APP CLEAVING ENZYME 1 / ASP 2 / ASP2 / BACE-1


Mass: 43761.312 Da / Num. of mol.: 1 / Fragment: RESIDUES 61-452 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-ZYE / N-{(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}-1-ETHYL-4-(2-OXOPYRROLIDIN-1-YL)-1H-INDOLE-6-CARBOXAMIDE


Mass: 554.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 223 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 354 TO GLN
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: 2.02 Å3/Da / Density % sol: 38.65 % / Description: DATASET WAS COLLECTED IN 2003
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: CRYSTALS GROWN BY VAPOUR DIFFUSION AT 20C USING STREAK SEEDING, WITH 10% PEG8000 AND 0.1M GLYCINE PH 3.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→44 Å
Details: FULL DATA PROCESSING AND SCALING STATISTICS NO LONGER AVAILABLE FOR THIS DATASET.
Rfactor% reflection
Rfree0.223 4 %
Rwork0.2 -
obs0.2 -
Refinement stepCycle: LAST / Resolution: 1.7→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 41 382 3357

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