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- PDB-3zlq: BACE2 XAPERONE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 3zlq
TitleBACE2 XAPERONE COMPLEX
Components
  • BETA-SECRETASE 2
  • XA4813
KeywordsHYDROLASE/IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome organization / melanosome membrane / 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 organization / melanosome membrane / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / endoplasmic reticulum / Golgi apparatus / 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 / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6T9 / Beta-secretase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsKuglstatter, A. / Stihle, M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Beta-Secretase (Bace1) Inhibitors with High in Vivo Efficacy Suitable for Clinical Evaluation in Alzheimer'S Disease.
Authors: Hilpert, H. / Guba, W. / Woltering, T.J. / Wostl, W. / Pinard, E. / Mauser, H. / Mayweg, A.V. / Rogers-Evans, M. / Humm, R. / Krummenacher, D. / Muser, T. / Schnider, C. / Jacobsen, H. / ...Authors: Hilpert, H. / Guba, W. / Woltering, T.J. / Wostl, W. / Pinard, E. / Mauser, H. / Mayweg, A.V. / Rogers-Evans, M. / Humm, R. / Krummenacher, D. / Muser, T. / Schnider, C. / Jacobsen, H. / Ozmen, L. / Bergadano, A. / Banner, D.W. / Hochstrasser, R. / Kuglstatter, A. / David-Pierson, P. / Fischer, H. / Polara, A. / Narquizian, R.
History
DepositionFeb 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Atomic model / Derived calculations / Other
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Oct 23, 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

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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: XA4813
D: XA4813
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2166
Polymers110,4004
Non-polymers8172
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-45.4 kcal/mol
Surface area45930 Å2
MethodPQS
Unit cell
Length a, b, c (Å)46.780, 210.983, 53.303
Angle α, β, γ (deg.)90.00, 105.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-SECRETASE 2 / ASPARTIC-LIKE PROTEASE 56 KDA / ASPARTYL PROTEASE 1 / ASP1 / ASP 1 / BETA-SITE AMYLOID PRECURSOR ...ASPARTIC-LIKE PROTEASE 56 KDA / ASPARTYL PROTEASE 1 / ASP1 / ASP 1 / BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 2 / BETA-SITE APP CLEAVING ENZYME 2 / DOWN REGION ASPARTIC PROTEASE / DRAP / MEMAPSIN-1 / MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 1 / THETA-SECRETASE / BACE2


Mass: 42047.355 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR, RESIDUES 75-460 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Z0, memapsin 1
#2: Antibody XA4813


Mass: 13152.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMESY4 / Production host: ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-6T9 / 5-Ethoxy-pyridine-2-carboxylic acid [3-((R)-2-amino-5,5-difluoro-4-methyl-5,6-dihydro-4H-[1,3]oxazin-4-yl)-4-fluoro-phenyl]-amide


Mass: 408.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19F3N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. ...THE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. THE MUTATION HERE IS E269A IN THE PDB FILE AND E331A IN THE DATA BANK SEQUENCE. ANTIBODY RAISED IN LLAMA AGAINST BACE2. V(HH) EXPRESSED IN E. COLI. WITH 6HIS AND EPEA TAG.

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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: 2.3 Å3/Da / Density % sol: 46.54 % / Description: NONE
Crystal growpH: 7 / Details: 25% PEG1500, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→46.26 Å / Num. obs: 67998 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.1→46.26 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.874 / SU B: 15.407 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29601 2596 5.1 %RANDOM
Rwork0.23825 ---
obs0.24123 48660 88.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20.66 Å2
2---1.28 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7361 0 58 159 7578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.027638
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.96110393
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0395961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02623.969320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.953151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2141540
X-RAY DIFFRACTIONr_chiral_restr0.1320.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215829
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 170 -
Rwork0.335 3475 -
obs--85.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.337-0.02480.02980.4133-0.080.198-0.0084-0.00170.0334-0.07970.00230.00120.0095-0.01240.00610.1523-0.0049-0.00570.07670.00420.0038-4.9681-21.404719.2013
20.1447-0.0503-0.05520.55590.18060.21440.0074-0.0094-0.0259-0.08520.0056-0.07080.00060.01-0.01310.1492-0.01060.01040.07150.00730.027314.33821.368618.2705
30.83130.34780.06771.0985-0.18640.5318-0.0007-0.0124-0.0506-0.0044-0.0024-0.03260.0641-0.00780.00310.1496-0.00310.00070.06920.01830.0078-6.0873-52.239537.1781
41.02770.45050.01630.70510.14940.4071-0.0083-0.03870.0066-0.05650.0137-0.0266-0.0596-0.0019-0.00540.1572-0.0104-0.02090.0758-0.00930.006615.650552.5535.5538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 397
2X-RAY DIFFRACTION2B15 - 397
3X-RAY DIFFRACTION3C160 - 271
4X-RAY DIFFRACTION4D160 - 271

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