data_2Y2A # _entry.id 2Y2A # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2Y2A PDBE EBI-46719 WWPDB D_1290046719 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1UOA unspecified 'AFTER 3NS' PDB 1TAW unspecified 'BOVINE TRYPSIN COMPLEXED TO APPI' PDB 2Y3J unspecified 'STRUCTURE OF SEGMENT AIIGLM FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 30-35)' PDB 1TKN unspecified 'SOLUTION STRUCTURE OF CAPPD*, AN INDEPENDENTLY FOLDEDEXTRACELLULAR DOMAIN OF HUMAN AMYLOID-BETA PRECURSORPROTEIN' PDB 1QCM unspecified 'AMYLOID BETA PEPTIDE (25-35), NMR, 20 STRUCTURES' PDB 1BA6 unspecified ;SOLUTION STRUCTURE OF THE METHIONINE-OXIDIZED AMYLOID BETA-PEPTIDE (1-40). DOES OXIDATION AFFECT CONFORMATIONAL SWITCHING? NMR, 10 STRUCTURES ; PDB 1QYT unspecified 'SOLUTION STRUCTURE OF FRAGMENT (25-35) OF BETA AMYLOIDPEPTIDE IN SDS MICELLAR SOLUTION' PDB 1BJB unspecified 'SOLUTION NMR STRUCTURE OF AMYLOID BETA[E16], RESIDUES 1-28, 14 STRUCTURES' PDB 2Y3L unspecified 'STRUCTURE OF SEGMENT MVGGVVIA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 35-42), ALTERNATE POLYMORPH 2' PDB 2Y3K unspecified 'STRUCTURE OF SEGMENT MVGGVVIA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 35-42), ALTERNATE POLYMORPH 1' PDB 1CA0 unspecified 'BOVINE CHYMOTRYPSIN COMPLEXED TO APPI' PDB 1BRC unspecified . PDB 1UO8 unspecified 'AFTER 2NS' PDB 1BA4 unspecified ;THE SOLUTION STRUCTURE OF AMYLOID BETA-PEPTIDE (1-40 ) IN A WATER-MICELLE ENVIRONMENT. IS THE MEMBRANE- SPANNING DOMAIN WHERE WE THINK IT IS? NMR, 10 STRUCTURES ; PDB 2WK3 unspecified 'CRYSTAL STRUCTURE OF HUMAN INSULIN-DEGRADING ENZYME IN COMPLEX WITH AMYLOID-BETA (1-42)' PDB 1AAP unspecified . PDB 1X11 unspecified 'X11 PTB DOMAIN' PDB 1QWP unspecified 'NMR ANALYSIS OF 25-35 FRAGMENT OF BETA AMYLOID PEPTIDE' PDB 1ZE9 unspecified ;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE COMPLEXED WITH A ZINC (II) CATION ; PDB 1QXC unspecified 'NMR STRUCTURE OF THE FRAGMENT 25-35 OF BETA AMYLOID PEPTIDEIN 20/80 V:V HEXAFLUOROISOPROPANOL/WATER MIXTURE' PDB 1IYT unspecified ;SOLUTION STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (1-42) ; PDB 1ZE7 unspecified ;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN WATER SOLUTION AT PH 6.5 ; PDB 2BEG unspecified ;3D STRUCTURE OF ALZHEIMER'S ABETA(1-42) FIBRILS ; PDB 1UOI unspecified 'AFTER 4NS' PDB 1AMB unspecified ;ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (RESIDUES 1 - 28) (NMR, MINIMIZED AVERAGE STRUCTURE) ; PDB 1RW6 unspecified 'HUMAN APP CORE DOMAIN' PDB 1UO7 unspecified 'MOLECULAR DYNAMICS SIMULATION OF AMYLOID BETA 1-42 ( PDB: 1IYT) IN WATER' PDB 1OWT unspecified ;STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID PRECURSORPROTEIN COPPER BINDING DOMAIN ; PDB 1AML unspecified ;THE ALZHEIMER'S DISEASE AMYLOID A4 PEPTIDE (RESIDUES 1 -40) ; PDB 1AMC unspecified ;ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (RESIDUES 1 - 28) (NMR, 5 STRUCTURES) ; PDB 1ZJD unspecified ;CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH KUNITZ PROTEASE INHIBITOR DOMAINOF PROTEASE NEXIN II ; PDB 2BP4 unspecified ;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN TFE-WATER (80-20) SOLUTION ; PDB 2BOM unspecified ;MODEL OF ALZHEIMER'S DISEASE AMYLOID-SS PEPTIDE BASED ON A RNA BINDING PROTEIN ; PDB 1BJC unspecified 'SOLUTION NMR STRUCTURE OF AMYLOID BETA[F16], RESIDUES 1-28, 15 STRUCTURES' PDB 2Y29 unspecified 'STRUCTURE OF SEGMENT KLVFFA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 16-21), ALTERNATE POLYMORPH III' PDB 1MWP unspecified 'N-TERMINAL DOMAIN OF THE AMYLOID PRECURSOR PROTEIN' PDB 1HZ3 unspecified ;ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10- 35) ; # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2Y2A _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2010-12-14 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Colletier, J.' 1 'Laganowsky, A.' 2 'Sawaya, M.R.' 3 'Eisenberg, D.' 4 # _citation.id primary _citation.title 'Molecular Basis for Amyloid-{Beta} Polymorphism.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 108 _citation.page_first 16938 _citation.page_last ? _citation.year 2011 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21949245 _citation.pdbx_database_id_DOI 10.1073/PNAS.1112600108 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Colletier, J.' 1 primary 'Laganowsky, A.' 2 primary 'Landau, M.' 3 primary 'Zhao, M.' 4 primary 'Soriaga, A.B.' 5 primary 'Goldschmidt, L.' 6 primary 'Flot, D.' 7 primary 'Cascio, D.' 8 primary 'Sawaya, M.R.' 9 primary 'Eisenberg, D.' 10 # _cell.entry_id 2Y2A _cell.length_a 9.580 _cell.length_b 11.850 _cell.length_c 42.470 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Y2A _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'AMYLOID BETA A4 PROTEIN' 724.909 1 ? ? 'SEGMENT KLVFFA, RESIDUES 687-692' ? 2 non-polymer syn 'ACETATE ION' 59.044 1 ? ? ? ? 3 water nat water 18.015 3 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;AMYLOID BETA PEPTIDE, ABPP, APPI, APP, ALZHEIMER DISEASE AMYLOID PROTEIN, CEREBRAL VASCULAR AMYLOID PEPTIDE, CVAP, PREA4, PROTEASE NEXIN-II, PN-II ; # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code KLVFFA _entity_poly.pdbx_seq_one_letter_code_can KLVFFA _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LYS n 1 2 LEU n 1 3 VAL n 1 4 PHE n 1 5 PHE n 1 6 ALA n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'HOMO SAPIENS' _pdbx_entity_src_syn.organism_common_name HUMAN _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A4_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P05067 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2Y2A _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P05067 _struct_ref_seq.db_align_beg 687 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 692 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 7 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ACT non-polymer . 'ACETATE ION' ? 'C2 H3 O2 -1' 59.044 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 HOH non-polymer . WATER ? 'H2 O' 18.015 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2Y2A _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.71 _exptl_crystal.density_percent_sol 28 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;AB16-21 FORM I CRYSTALS WERE OBTAINED AFTER THE SEGMENT WAS DISSOLVED IN WATER AT 5 MG/ML AND MIXED WITH 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 5.5, 45 % V/V MPD ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.87260 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID23-2' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID23-2 _diffrn_source.pdbx_wavelength 0.87260 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2Y2A _reflns.observed_criterion_sigma_I 3.5 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 21.20 _reflns.d_resolution_high 1.90 _reflns.number_obs 392 _reflns.number_all ? _reflns.percent_possible_obs 85.0 _reflns.pdbx_Rmerge_I_obs 0.15 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 7.40 _reflns.B_iso_Wilson_estimate 19.348 _reflns.pdbx_redundancy 3.5 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.90 _reflns_shell.d_res_low 2.20 _reflns_shell.percent_possible_all 75.7 _reflns_shell.Rmerge_I_obs 0.36 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.85 _reflns_shell.pdbx_redundancy 3.9 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2Y2A _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 372 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 11.41 _refine.ls_d_res_high 1.91 _refine.ls_percent_reflns_obs 85.03 _refine.ls_R_factor_obs 0.20837 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20640 _refine.ls_R_factor_R_free 0.24787 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 20 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.946 _refine.correlation_coeff_Fo_to_Fc_free 0.962 _refine.B_iso_mean 16.442 _refine.aniso_B[1][1] -4.28 _refine.aniso_B[2][2] 22.62 _refine.aniso_B[3][3] -18.34 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.059 _refine.pdbx_overall_ESU_R_Free 0.043 _refine.overall_SU_ML 0.074 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 2.823 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 52 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 59 _refine_hist.d_res_high 1.91 _refine_hist.d_res_low 11.41 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.020 0.023 ? 56 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.703 2.029 ? 73 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 10.614 5.000 ? 5 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 4.237 20.000 ? 2 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 11.363 15.000 ? 9 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.121 0.200 ? 8 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 42 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.906 _refine_ls_shell.d_res_low 1.954 _refine_ls_shell.number_reflns_R_work 12 _refine_ls_shell.R_factor_R_work 0.226 _refine_ls_shell.percent_reflns_obs 40.63 _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2Y2A _struct.title 'Structure of segment KLVFFA from the amyloid-beta peptide (Ab, residues 16-21), alternate polymorph I' _struct.pdbx_descriptor 'AMYLOID BETA A4 PROTEIN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2Y2A _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' _struct_keywords.text 'PROTEIN FIBRIL, ALZHEIMER DISEASE' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'BINDING SITE FOR RESIDUE ACT A 1008' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 LYS A 1 ? LYS A 2 . ? 4_435 ? 2 AC1 5 LYS A 1 ? LYS A 2 . ? 2_445 ? 3 AC1 5 PHE A 5 ? PHE A 6 . ? 1_555 ? 4 AC1 5 ALA A 6 ? ALA A 7 . ? 1_555 ? 5 AC1 5 HOH C . ? HOH A 2003 . ? 1_555 ? # _database_PDB_matrix.entry_id 2Y2A _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2Y2A _atom_sites.fract_transf_matrix[1][1] 0.104384 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.084388 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.023546 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . LYS A 1 1 ? -1.334 1.852 -7.753 1.00 12.07 ? 2 LYS A N 1 ATOM 2 C CA . LYS A 1 1 ? -1.943 0.655 -7.101 1.00 11.60 ? 2 LYS A CA 1 ATOM 3 C C . LYS A 1 1 ? -1.325 0.528 -5.746 1.00 11.69 ? 2 LYS A C 1 ATOM 4 O O . LYS A 1 1 ? -0.084 0.407 -5.672 1.00 11.66 ? 2 LYS A O 1 ATOM 5 C CB . LYS A 1 1 ? -1.631 -0.609 -7.915 1.00 12.71 ? 2 LYS A CB 1 ATOM 6 C CG . LYS A 1 1 ? -1.974 -1.892 -7.241 1.00 15.55 ? 2 LYS A CG 1 ATOM 7 C CD . LYS A 1 1 ? -2.102 -3.103 -8.198 1.00 16.66 ? 2 LYS A CD 1 ATOM 8 C CE . LYS A 1 1 ? -0.815 -3.611 -8.824 1.00 15.73 ? 2 LYS A CE 1 ATOM 9 N NZ . LYS A 1 1 ? -1.061 -4.900 -9.632 1.00 13.21 ? 2 LYS A NZ 1 ATOM 10 N N . LEU A 1 2 ? -2.165 0.536 -4.686 1.00 9.76 ? 3 LEU A N 1 ATOM 11 C CA . LEU A 1 2 ? -1.709 0.188 -3.332 1.00 8.84 ? 3 LEU A CA 1 ATOM 12 C C . LEU A 1 2 ? -2.242 -1.190 -2.970 1.00 8.55 ? 3 LEU A C 1 ATOM 13 O O . LEU A 1 2 ? -3.433 -1.466 -3.093 1.00 8.36 ? 3 LEU A O 1 ATOM 14 C CB . LEU A 1 2 ? -2.254 1.169 -2.282 1.00 8.38 ? 3 LEU A CB 1 ATOM 15 C CG . LEU A 1 2 ? -2.026 0.948 -0.760 1.00 7.99 ? 3 LEU A CG 1 ATOM 16 C CD1 . LEU A 1 2 ? -0.558 1.217 -0.331 1.00 7.38 ? 3 LEU A CD1 1 ATOM 17 C CD2 . LEU A 1 2 ? -2.946 1.828 0.075 1.00 7.69 ? 3 LEU A CD2 1 ATOM 18 N N . VAL A 1 3 ? -1.364 -2.007 -2.421 1.00 8.06 ? 4 VAL A N 1 ATOM 19 C CA . VAL A 1 3 ? -1.802 -3.187 -1.756 1.00 8.60 ? 4 VAL A CA 1 ATOM 20 C C . VAL A 1 3 ? -1.169 -3.244 -0.378 1.00 9.07 ? 4 VAL A C 1 ATOM 21 O O . VAL A 1 3 ? 0.040 -3.304 -0.239 1.00 10.22 ? 4 VAL A O 1 ATOM 22 C CB . VAL A 1 3 ? -1.428 -4.429 -2.531 1.00 7.98 ? 4 VAL A CB 1 ATOM 23 C CG1 . VAL A 1 3 ? -2.051 -5.716 -1.886 1.00 7.84 ? 4 VAL A CG1 1 ATOM 24 C CG2 . VAL A 1 3 ? -1.750 -4.301 -4.025 1.00 8.19 ? 4 VAL A CG2 1 ATOM 25 N N . PHE A 1 4 ? -2.014 -3.237 0.640 1.00 11.83 ? 5 PHE A N 1 ATOM 26 C CA . PHE A 1 4 ? -1.588 -3.380 2.032 1.00 12.27 ? 5 PHE A CA 1 ATOM 27 C C . PHE A 1 4 ? -2.275 -4.573 2.662 1.00 13.82 ? 5 PHE A C 1 ATOM 28 O O . PHE A 1 4 ? -3.521 -4.672 2.575 1.00 15.79 ? 5 PHE A O 1 ATOM 29 C CB . PHE A 1 4 ? -1.980 -2.139 2.822 1.00 11.97 ? 5 PHE A CB 1 ATOM 30 C CG . PHE A 1 4 ? -1.754 -2.267 4.292 1.00 11.24 ? 5 PHE A CG 1 ATOM 31 C CD1 . PHE A 1 4 ? -0.509 -2.005 4.837 1.00 13.30 ? 5 PHE A CD1 1 ATOM 32 C CD2 . PHE A 1 4 ? -2.784 -2.614 5.127 1.00 10.94 ? 5 PHE A CD2 1 ATOM 33 C CE1 . PHE A 1 4 ? -0.320 -2.088 6.234 1.00 13.41 ? 5 PHE A CE1 1 ATOM 34 C CE2 . PHE A 1 4 ? -2.591 -2.745 6.500 1.00 11.77 ? 5 PHE A CE2 1 ATOM 35 C CZ . PHE A 1 4 ? -1.365 -2.458 7.047 1.00 11.58 ? 5 PHE A CZ 1 ATOM 36 N N . PHE A 1 5 ? -1.476 -5.455 3.275 1.00 14.81 ? 6 PHE A N 1 ATOM 37 C CA . PHE A 1 5 ? -1.984 -6.541 4.123 1.00 15.73 ? 6 PHE A CA 1 ATOM 38 C C . PHE A 1 5 ? -1.218 -6.607 5.435 1.00 16.89 ? 6 PHE A C 1 ATOM 39 O O . PHE A 1 5 ? -0.016 -6.875 5.416 1.00 13.20 ? 6 PHE A O 1 ATOM 40 C CB . PHE A 1 5 ? -1.848 -7.895 3.449 1.00 14.69 ? 6 PHE A CB 1 ATOM 41 C CG . PHE A 1 5 ? -2.572 -8.988 4.176 1.00 17.56 ? 6 PHE A CG 1 ATOM 42 C CD1 . PHE A 1 5 ? -3.928 -9.217 3.932 1.00 16.39 ? 6 PHE A CD1 1 ATOM 43 C CD2 . PHE A 1 5 ? -1.910 -9.768 5.145 1.00 20.27 ? 6 PHE A CD2 1 ATOM 44 C CE1 . PHE A 1 5 ? -4.613 -10.201 4.614 1.00 18.91 ? 6 PHE A CE1 1 ATOM 45 C CE2 . PHE A 1 5 ? -2.602 -10.752 5.845 1.00 21.33 ? 6 PHE A CE2 1 ATOM 46 C CZ . PHE A 1 5 ? -3.959 -10.975 5.552 1.00 18.84 ? 6 PHE A CZ 1 ATOM 47 N N . ALA A 1 6 ? -1.907 -6.448 6.572 1.00 21.78 ? 7 ALA A N 1 ATOM 48 C CA . ALA A 1 6 ? -1.277 -6.712 7.898 1.00 23.97 ? 7 ALA A CA 1 ATOM 49 C C . ALA A 1 6 ? -2.066 -7.660 8.834 1.00 32.80 ? 7 ALA A C 1 ATOM 50 O O . ALA A 1 6 ? -3.245 -7.905 8.595 1.00 29.64 ? 7 ALA A O 1 ATOM 51 C CB . ALA A 1 6 ? -0.953 -5.441 8.593 1.00 26.09 ? 7 ALA A CB 1 ATOM 52 O OXT . ALA A 1 6 ? -1.550 -8.249 9.820 1.00 33.63 ? 7 ALA A OXT 1 HETATM 53 C C . ACT B 2 . ? -3.334 -11.524 9.718 1.00 35.51 ? 1008 ACT A C 1 HETATM 54 O O . ACT B 2 . ? -3.296 -12.741 10.153 1.00 36.47 ? 1008 ACT A O 1 HETATM 55 O OXT . ACT B 2 . ? -4.406 -10.873 9.502 1.00 26.04 ? 1008 ACT A OXT 1 HETATM 56 C CH3 . ACT B 2 . ? -2.025 -10.826 9.449 1.00 27.90 ? 1008 ACT A CH3 1 HETATM 57 O O . HOH C 3 . ? -2.149 4.522 -7.326 1.00 36.53 ? 2001 HOH A O 1 HETATM 58 O O . HOH C 3 . ? -3.671 -6.911 -8.668 1.00 39.72 ? 2002 HOH A O 1 HETATM 59 O O . HOH C 3 . ? -1.183 -14.039 10.669 1.00 25.69 ? 2003 HOH A O 1 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 LYS 1 2 2 LYS LYS A . n A 1 2 LEU 2 3 3 LEU LEU A . n A 1 3 VAL 3 4 4 VAL VAL A . n A 1 4 PHE 4 5 5 PHE PHE A . n A 1 5 PHE 5 6 6 PHE PHE A . n A 1 6 ALA 6 7 7 ALA ALA A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 ACT 1 1008 1008 ACT ACT A . C 3 HOH 1 2001 2001 HOH HOH A . C 3 HOH 2 2002 2002 HOH HOH A . C 3 HOH 3 2003 2003 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2011-10-26 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.6.0081 ? 1 XDS 'data reduction' . ? 2 XSCALE 'data scaling' . ? 3 PHASER phasing . ? 4 # _pdbx_entry_details.entry_id 2Y2A _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;IN VIVO AMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTIC PRODUCT OF THE AMYLOID PRECURSOR PROTEIN (APP). AB SEGMENT 16-KLVFFA-21 CORRESPONDS TO RESIDUES 687-692 OF APP ; # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 2001 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 2002 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 1_565 _pdbx_validate_symm_contact.dist 2.07 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ACETATE ION' ACT 3 water HOH #