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- PDB-3zks: BACE2 XAPERONE COMPLEX WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 3zks
TitleBACE2 XAPERONE COMPLEX WITH INHIBITOR
Components
  • BETA-SECRETASE 2
  • XA4813
KeywordsHYDROLASE/IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM COMPLEX / INHIBITOR / NANOBODY
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 / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-WZV / Beta-secretase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsBanner, D.W. / Kuglstatter, A. / Benz, J. / Stihle, M. / Ruf, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones
Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / ...Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / Kuglstatter, A. / Kusznir, E. / Laeremans, T. / Matile, H. / Miscenic, C. / Rufer, A. / Schlatter, D. / Steyeart, J. / Stihle, M. / Thoma, R. / Weber, M. / Ruf, A.
History
DepositionJan 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-SECRETASE 2
D: XA4813
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6933
Polymers55,2582
Non-polymers4351
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-5.3 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.101, 74.764, 108.721
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 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: 42105.391 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 75-460
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.: 1
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-WZV / 5-(2,2,2-Trifluoro-ethoxy)-pyridine-2-carboxylic acid [3-((S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydro-pyrimidin-4-yl)-phenyl]-amide


Mass: 435.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20F3N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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. 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: 2.49 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growDetails: 25% PEG1500

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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: Sep 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→44.4 Å / Num. obs: 28977 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.2
Reflection shellResolution: 2.11→2.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.26 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKQ

3zkq


Resolution: 2.11→44.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.7 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.HYDROGENS WERE USED BUT NOT OUTPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26041 1383 5.1 %RANDOM
Rwork0.2085 ---
obs0.21115 25928 88.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.301 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---1.97 Å20 Å2
3---2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.11→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 31 150 3816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023796
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9615166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8895472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18523.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53815589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.321520
X-RAY DIFFRACTIONr_chiral_restr0.0950.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212898
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: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 82 -
Rwork0.317 1878 -
obs--87.74 %

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