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- PDB-6dmi: A multiconformer ligand model of 5T5 bound to BACE-1 -

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Basic information

Entry
Database: PDB / ID: 6dmi
TitleA multiconformer ligand model of 5T5 bound to BACE-1
ComponentsBeta-secretase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / complex / multiconformer model / HYDROLASE / 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 / 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
Chem-5T5 / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsHudson, B.M. / van Zundert, G. / Keedy, D.A. / Fonseca, R. / Heliou, A. / Suresh, P. / Borrelli, K. / Day, T. / Fraser, J.S. / van den Bedem, H.
Citation
Journal: J. Med. Chem. / Year: 2018
Title: qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
Authors: van Zundert, G.C.P. / Hudson, B.M. / de Oliveira, S.H.P. / Keedy, D.A. / Fonseca, R. / Heliou, A. / Suresh, P. / Borrelli, K. / Day, T. / Fraser, J.S. / van den Bedem, H.
#1: Journal: J. Med. Chem. / Year: 2016
Title: A Real-World Perspective on Molecular Design.
Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 0THIS ENTRY 6DMI REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5EZX, DETERMINED BY . ...THIS ENTRY 6DMI REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5EZX, DETERMINED BY .KUHN,W.GUBA,J.HERT,D.BANNER,C.BISSANTZ,S.CECCARELLI,W.HAAP,M.KORNER,A.KUGLSTATTER,C.LERNER,P.MATTEI,W.NEIDHART,E.PINARD,M.G.RUDOLPH,T.SCHULZ-GASCH,T.WOLTERING,M.STAHL

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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)43,9445
Polymers43,4121
Non-polymers5324
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.320, 102.320, 169.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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: 43411.895 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-5T5 / [(1~{R},2~{R})-2-[(4~{S})-2-azanyl-4-[4-[bis(fluoranyl)methoxy]phenyl]-5~{H}-1,3-oxazol-4-yl]cyclopropyl]-(5-chloranylpyridin-3-yl)methanone


Mass: 407.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClF2N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.96 Å3/Da / Density % sol: 58.38 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5EZX
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.5M SODIUM FORMATE, 100MM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.73 Å / Num. obs: 41604 / % possible obs: 98.8 % / Redundancy: 5.33 % / Net I/σ(I): 14.37
Reflection shellResolution: 1.9→2 Å

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Processing

Software
NameVersionClassification
PHENIX1.11_2558refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.9→47.704 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 23
RfactorNum. reflection% reflection
Rfree0.2258 2000 4.81 %
Rwork0.1924 --
obs0.194 41604 98.91 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 97.06 Å2 / Biso mean: 34.4303 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: final / Resolution: 1.9→47.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 90 340 3371
Biso mean--30.65 40.22 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143185
X-RAY DIFFRACTIONf_angle_d1.1714334
X-RAY DIFFRACTIONf_chiral_restr0.07461
X-RAY DIFFRACTIONf_plane_restr0.007558
X-RAY DIFFRACTIONf_dihedral_angle_d6.7623136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94760.31631390.28782754289398
1.9476-2.00020.28681390.25872743288298
2.0002-2.05910.31241400.24392770291099
2.0591-2.12550.25111380.22872755289399
2.1255-2.20150.28321410.21652784292599
2.2015-2.28960.22021400.21312771291199
2.2896-2.39380.28671420.20592807294999
2.3938-2.520.26481410.20642806294799
2.52-2.67790.26051430.20022832297599
2.6779-2.88470.26121440.20382835297999
2.8847-3.17490.23041440.190828573001100
3.1749-3.63420.19941460.174828913037100
3.6342-4.57810.18711490.153629373086100
4.5781-47.71880.18191540.18153062321698

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