data_2BP4 # _entry.id 2BP4 # _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 2BP4 PDBE EBI-23670 WWPDB D_1290023670 # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2005-04-21 _pdbx_database_PDB_obs_spr.pdb_id 2BP4 _pdbx_database_PDB_obs_spr.replace_pdb_id 1O6N _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1AAP unspecified . PDB 1AMB unspecified ;ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE ( RESIDUES 1 - 28) (NMR, MINIMIZED AVERAGE STRUCTURE) ; PDB 1AMC unspecified ;ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE ( RESIDUES 1 - 28) (NMR, 5 STRUCTURES) ; PDB 1AML unspecified 'THE ALZHEIMER`S DISEASE AMYLOID A4 PEPTIDE (RESIDUES 1-40)' 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 1BA6 unspecified ;SOLUTION STRUCTURE OF THE METHIONINE-OXIDIZED AMYLOID BETA-PEPTIDE (1-40). DOES OXIDATION AFFECT CONFORMATIONAL SWITCHING? NMR , 10 STRUCTURES ; PDB 1BJB unspecified 'SOLUTION NMR STRUCTURE OF AMYLOID BETA[E16 ], RESIDUES 1-28, 14 STRUCTURES' PDB 1BJC unspecified 'SOLUTION NMR STRUCTURE OF AMYLOID BETA[F16 ], RESIDUES 1-28, 15 STRUCTURES' PDB 1BRC unspecified . PDB 1CA0 unspecified 'BOVINE CHYMOTRYPSIN COMPLEXED TO APPI' PDB 1HZ3 unspecified ;ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE ( RESIDUES 10-35) ; PDB 1IYT unspecified ;SOLUTION STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (1-42) ; PDB 1MWP unspecified 'N-TERMINAL DOMAIN OF THE AMYLOID PRECURSOR PROTEIN' PDB 1O6N unspecified 'ABETA(1-16) FRAGMENT OF THE AMYLOID PEPTIDE' PDB 1OWT unspecified ;STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID PRECURSORPROTEIN COPPER BINDING DOMAIN ; PDB 1QCM unspecified 'AMYLOID BETA PEPTIDE (25-35), NMR, 20 STRUCTURES' PDB 1QWP unspecified 'NMR ANALYSIS OF 25-35 FRAGMENT OF BETA AMYLOID PEPTIDE' PDB 1QXC unspecified 'NMR STRUCTURE OF THE FRAGMENT 25-35 OF BETA AMYLOID PEPTIDEIN 20/80 V:V HEXAFLUOROISOPROPANOL/WATER MIXTURE' PDB 1QYT unspecified 'SOLUTION STRUCTURE OF FRAGMENT (25-35) OF BETA AMYLOIDPEPTIDE IN SDS MICELLAR SOLUTION' PDB 1TAW unspecified 'BOVINE TRYPSIN COMPLEXED TO APPI' PDB 1TKN unspecified 'SOLUTION STRUCTURE OF CAPPD*, AN INDEPENDENTLY FOLDEDEXTRACELLULAR DOMAIN OF HUMAN AMYLOID- BETA PRECURSORPROTEIN' PDB 1UO7 unspecified 'MOLECULAR DYNAMICS SIMULATION OF AMYLOID BETA 1-42 (PDB: 1IYT) IN WATER' PDB 1UO8 unspecified 'AFTER 2NS' PDB 1UOA unspecified 'AFTER 3NS' PDB 1UOI unspecified 'AFTER 4NS' PDB 2BOM unspecified ;MODEL OF ALZHEIMER'S DISEASE AMYLOID-SS PEPTIDE BASED ON A RNA BINDING PROTEIN ; # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2BP4 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2005-04-18 _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 'Zirah, S.' 1 'Kozin, S.A.' 2 'Mazur, A.K.' 3 'Blond, A.' 4 'Cheminant, M.' 5 'Segalas-Milazzo, I.' 6 'Debey, P.' 7 'Rebuffat, S.' 8 # _citation.id primary _citation.title 'Structural Changes of Region 1-16 of the Alzheimer Disease Amyloid Beta-Peptide Upon Zinc Binding and in Vitro Aging.' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 281 _citation.page_first 2151 _citation.page_last ? _citation.year 2006 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16301322 _citation.pdbx_database_id_DOI 10.1074/JBC.M504454200 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Zirah, S.' 1 primary 'Kozin, S.A.' 2 primary 'Mazur, A.K.' 3 primary 'Blond, A.' 4 primary 'Cheminant, M.' 5 primary 'Segalas-Milazzo, I.' 6 primary 'Debey, P.' 7 primary 'Rebuffat, S.' 8 # _cell.entry_id 2BP4 _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BP4 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'AMYLOID BETA A4 PROTEIN' _entity.formula_weight 1960.047 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ;16-MER FRAGMENT BETWEEN THE BETA AND ALPHA SECRETASES CLEAVAGE SITES OF ALZHEIMER'S DISEASE AMYLOID A4 PROTEIN, RESIDUES 672-687 ; _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name ;APP, ABPP, ALZHEIMER'S DISEASE AMYLOID A4 PROTEIN, CEREBRAL VASCULAR AMYLOID PEPTIDE, CVAP, PROTEASE NEXIN-II, PN-II, APPI, PREA4 ; # _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 DAEFRHDSGYEVHHQK _entity_poly.pdbx_seq_one_letter_code_can DAEFRHDSGYEVHHQK _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 ASP n 1 2 ALA n 1 3 GLU n 1 4 PHE n 1 5 ARG n 1 6 HIS n 1 7 ASP n 1 8 SER n 1 9 GLY n 1 10 TYR n 1 11 GLU n 1 12 VAL n 1 13 HIS n 1 14 HIS n 1 15 GLN n 1 16 LYS 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 2BP4 _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 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P05067 _struct_ref_seq.db_align_beg 672 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 687 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 16 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 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 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 DQF-COSY 1 2 1 '2D TOCSY 2D NOESY' 1 3 1 HSQC 1 4 1 HMBC 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298.0 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1.0 _pdbx_nmr_exptl_sample_conditions.pH 3.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '80 % TFE-D2OH / 20 % H2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength 1 Avance Bruker 400 2 DMX Bruker 600 # _pdbx_nmr_refine.entry_id 2BP4 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details 'REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2BP4 _pdbx_nmr_details.text 'THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES' # _pdbx_nmr_ensemble.entry_id 2BP4 _pdbx_nmr_ensemble.conformers_calculated_total_number 1000 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'MINIMAL TARGET FUNCTION' # _pdbx_nmr_representative.entry_id 2BP4 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria ? # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement ICMD ? 'ALEXEY K. MAZUR' 1 'structure solution' ICMD 2.7 ? 2 # _exptl.entry_id 2BP4 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2BP4 _struct.title ;Zinc-binding domain of Alzheimer's disease amyloid beta-peptide in TFE-water (80-20) solution ; _struct.pdbx_descriptor 'AMYLOID BETA A4 PROTEIN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2BP4 _struct_keywords.pdbx_keywords 'AMYLOID PEPTIDE' _struct_keywords.text ;HELIX, ALZHEIMER'S DISEASE, AMYLOID, AMYLOID PEPTIDE, BETA-AMYLOID PROTEIN ; # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id ASP _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 1 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id GLN _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 15 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ASP _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 1 _struct_conf.end_auth_comp_id GLN _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 15 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 15 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 2BP4 _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 2BP4 _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _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 H N O # 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 ASP 1 1 1 ASP ASP A . n A 1 2 ALA 2 2 2 ALA ALA A . n A 1 3 GLU 3 3 3 GLU GLU A . n A 1 4 PHE 4 4 4 PHE PHE A . n A 1 5 ARG 5 5 5 ARG ARG A . n A 1 6 HIS 6 6 6 HIS HIS A . n A 1 7 ASP 7 7 7 ASP ASP A . n A 1 8 SER 8 8 8 SER SER A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 TYR 10 10 10 TYR TYR A . n A 1 11 GLU 11 11 11 GLU GLU A . n A 1 12 VAL 12 12 12 VAL VAL A . n A 1 13 HIS 13 13 13 HIS HIS A . n A 1 14 HIS 14 14 14 HIS HIS A . n A 1 15 GLN 15 15 15 GLN GLN A . n A 1 16 LYS 16 16 16 LYS LYS A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2005-04-21 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 # _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_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' # _pdbx_entry_details.entry_id 2BP4 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'PEPTIDE FRAGMENT 672-687' # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 5 GLN A 15 ? ? -91.10 45.11 2 8 HIS A 14 ? ? -104.97 59.17 3 11 GLN A 15 ? ? -84.46 45.36 4 12 GLN A 15 ? ? -87.59 46.35 5 14 HIS A 14 ? ? -95.48 53.09 6 17 HIS A 14 ? ? -110.68 60.45 7 18 HIS A 14 ? ? -101.43 53.24 8 19 HIS A 14 ? ? -95.78 46.56 9 20 HIS A 14 ? ? -92.81 -71.08 #