data_8ZD7 # _entry.id 8ZD7 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.406 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 8ZD7 pdb_00008zd7 10.2210/pdb8zd7/pdb WWPDB D_1300047536 ? ? BMRB 36663 ? 10.13018/BMR36663 # 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 _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-04-30 ? 2 'Structure model' 2 0 2025-11-12 ? # _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 ? _pdbx_audit_revision_details.details ? # 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' 'Atomic model' 2 2 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' atom_site 2 2 'Structure model' citation 3 2 'Structure model' citation_author # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.journal_volume' 7 2 'Structure model' '_citation.page_first' 8 2 'Structure model' '_citation.page_last' 9 2 'Structure model' '_citation.pdbx_database_id_DOI' 10 2 'Structure model' '_citation.pdbx_database_id_PubMed' 11 2 'Structure model' '_citation.title' 12 2 'Structure model' '_citation.year' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr . _pdbx_database_status.entry_id 8ZD7 _pdbx_database_status.recvd_initial_deposition_date 2024-05-01 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs . _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible N # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB . 8ZD2 unspecified BMRB 'NMR structure of the CGG-dsDNA-sND complex' 36663 unspecified # _pdbx_contact_author.id 2 _pdbx_contact_author.email kojima-chojiro-xk@ynu.ac.jp _pdbx_contact_author.name_first Chojiro _pdbx_contact_author.name_last Kojima _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-2723-8249 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Sakurabayashi, S.' 1 0000-0001-6561-2356 'Furuita, K.' 2 0000-0002-9272-0026 'Yamada, T.' 3 0000-0003-3275-415X 'Nomura, M.' 4 ? 'Nakatani, K.' 5 0000-0002-1705-5265 'Kojima, C.' 6 0000-0003-2723-8249 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 147 _citation.language ? _citation.page_first 14254 _citation.page_last 14269 _citation.title ;NMR-Based Rational Drug Design of G:G Mismatch DNA Binding Ligand Trapping Transient Complex via Disruption of a Key Allosteric Interaction. ; _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.4c17538 _citation.pdbx_database_id_PubMed 40245052 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sakurabayashi, S.' 1 0000-0001-6561-2356 primary 'Furuita, K.' 2 ? primary 'Yamada, T.' 3 0000-0003-3275-415X primary 'Sugiura, N.' 4 ? primary 'Nomura, M.' 5 ? primary 'Nakane, T.' 6 ? primary 'Kawamoto, A.' 7 ? primary 'Kurisu, G.' 8 ? primary 'Miyanoiri, Y.' 9 0000-0001-6889-5160 primary 'Fujiwara, T.' 10 0000-0001-7739-3525 primary 'Nakatani, K.' 11 0000-0002-1705-5265 primary 'Kojima, C.' 12 0000-0003-2723-8249 # 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 ;DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3') ; 3382.236 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3') ; 3364.208 1 ? ? ? ? 3 non-polymer syn '~{N}-(7-methyl-1,8-naphthyridin-2-yl)-2-[[2-[(7-methyl-1,8-naphthyridin-2-yl)amino]-2-oxidanylidene-ethyl]amino]ethanamide' 415.448 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DC)(DT)(DA)(DA)(DC)(DG)(DG)(DA)(DA)(DT)(DG)' CTAACGGAATG 1 ? 2 polydeoxyribonucleotide no no '(DC)(DA)(DT)(DT)(DC)(DG)(DG)(DT)(DT)(DA)(DG)' CATTCGGTTAG 2 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name '~{N}-(7-methyl-1,8-naphthyridin-2-yl)-2-[[2-[(7-methyl-1,8-naphthyridin-2-yl)amino]-2-oxidanylidene-ethyl]amino]ethanamide' _pdbx_entity_nonpoly.comp_id A1L1R # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DT n 1 3 DA n 1 4 DA n 1 5 DC n 1 6 DG n 1 7 DG n 1 8 DA n 1 9 DA n 1 10 DT n 1 11 DG n 2 1 DC n 2 2 DA n 2 3 DT n 2 4 DT n 2 5 DC n 2 6 DG n 2 7 DG n 2 8 DT n 2 9 DT n 2 10 DA n 2 11 DG n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 11 'Homo sapiens' ? 9606 ? 2 1 sample 1 11 'Homo sapiens' ? 9606 ? # 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 A1L1R non-polymer . '~{N}-(7-methyl-1,8-naphthyridin-2-yl)-2-[[2-[(7-methyl-1,8-naphthyridin-2-yl)amino]-2-oxidanylidene-ethyl]amino]ethanamide' ? 'C22 H21 N7 O2' 415.448 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # 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 DC 1 1 1 DC CYT 1 . n A 1 2 DT 2 2 2 DT THY 1 . n A 1 3 DA 3 3 3 DA ADE 1 . n A 1 4 DA 4 4 4 DA ADE 1 . n A 1 5 DC 5 5 5 DC CYT 1 . n A 1 6 DG 6 6 6 DG GUA 1 . n A 1 7 DG 7 7 7 DG GUA 1 . n A 1 8 DA 8 8 8 DA ADE 1 . n A 1 9 DA 9 9 9 DA ADE 1 . n A 1 10 DT 10 10 10 DT THY 1 . n A 1 11 DG 11 11 11 DG GUA 1 . n B 2 1 DC 1 12 12 DC CYT 2 . n B 2 2 DA 2 13 13 DA ADE 2 . n B 2 3 DT 3 14 14 DT THY 2 . n B 2 4 DT 4 15 15 DT THY 2 . n B 2 5 DC 5 16 16 DC CYT 2 . n B 2 6 DG 6 17 17 DG GUA 2 . n B 2 7 DG 7 18 18 DG GUA 2 . n B 2 8 DT 8 19 19 DT THY 2 . n B 2 9 DT 9 20 20 DT THY 2 . n B 2 10 DA 10 21 21 DA ADE 2 . n B 2 11 DG 11 22 22 DG GUA 2 . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id A1L1R _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id A1L1R _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id A1L1R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 23 _pdbx_nonpoly_scheme.pdb_mon_id A1L1R _pdbx_nonpoly_scheme.auth_mon_id SND _pdbx_nonpoly_scheme.pdb_strand_id 2 _pdbx_nonpoly_scheme.pdb_ins_code . # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8ZD7 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 8ZD7 _struct.title 'NMR structure of the CGG-dsDNA-sND complex' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8ZD7 _struct_keywords.text 'mismatched base pair naphthyridine fragile X syndrome CGG repeat repeat expansion diseases, DNA' _struct_keywords.pdbx_keywords DNA # 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 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 8ZD7 8ZD7 ? 1 ? 1 2 PDB 8ZD7 8ZD7 ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 8ZD7 1 1 ? 11 ? 8ZD7 1 ? 11 ? 1 11 2 2 8ZD7 2 1 ? 11 ? 8ZD7 12 ? 22 ? 12 22 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'NMR Distance Restraints' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _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] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 11 N1 ? ? 1 DC 1 2 DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 11 O6 ? ? 1 DC 1 2 DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 11 N2 ? ? 1 DC 1 2 DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 10 N1 ? ? 1 DT 2 2 DA 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 10 N6 ? ? 1 DT 2 2 DA 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 9 N3 ? ? 1 DA 3 2 DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 9 O4 ? ? 1 DA 3 2 DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 8 N3 ? ? 1 DA 4 2 DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 8 O4 ? ? 1 DA 4 2 DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 7 N1 ? ? 1 DC 5 2 DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 7 O6 ? ? 1 DC 5 2 DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 7 N2 ? ? 1 DC 5 2 DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 5 N3 ? ? 1 DG 7 2 DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 5 O2 ? ? 1 DG 7 2 DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 5 N4 ? ? 1 DG 7 2 DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 4 N3 ? ? 1 DA 8 2 DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 4 O4 ? ? 1 DA 8 2 DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 3 N3 ? ? 1 DA 9 2 DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 3 O4 ? ? 1 DA 9 2 DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 2 N1 ? ? 1 DT 10 2 DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 2 N6 ? ? 1 DT 10 2 DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? ? 1 DG 11 2 DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? ? 1 DG 11 2 DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 1 N4 ? ? 1 DG 11 2 DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_entry_details.entry_id 8ZD7 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.60 2 2 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.58 3 4 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.58 4 8 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.57 5 9 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.57 6 10 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.55 7 12 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 8 15 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 9 16 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 10 17 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 11 18 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 12 19 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 13 20 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 14 21 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.54 15 23 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.58 16 24 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 17 27 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.59 18 28 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.58 19 29 O2 1 DC 5 ? ? H22 2 DG 18 ? ? 1.56 # _pdbx_nmr_ensemble.entry_id 8ZD7 _pdbx_nmr_ensemble.conformers_calculated_total_number 150 _pdbx_nmr_ensemble.conformers_submitted_total_number 30 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 8ZD7 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 ;2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl, 95% H2O/5% D2O ; '95% H2O/5% D2O' CGG-dsDNA-sND solution ? 2 ;2.0 mM None DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3'), 2.0 mM None DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3'), 2.0 mM None sND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl, 12 mg/mL None Pf1, 95% H2O/5% D2O ; '95% H2O/5% D2O' 'CGG-dsDNA-sND with pf1' solution 'containing 12 mg/mL of pf1' # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 ;DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3') ; 2.0 ? mM None 1 ;DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3') ; 2.0 ? mM None 1 sND 2.0 ? mM None 1 'sodium phosphate (pH 6.8)' 20 ? mM None 1 NaCl 100 ? mM None 2 ;DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3') ; 2.0 ? mM None 2 ;DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3') ; 2.0 ? mM None 2 sND 2.0 ? mM None 2 'sodium phosphate (pH 6.8)' 20 ? mM None 2 NaCl 100 ? mM None 2 Pf1 12 ? mg/mL None # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 303 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.ionic_strength 120 _pdbx_nmr_exptl_sample_conditions.details 'For distance constraints' _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label 'condition 1' _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-1H NOESY' 2 isotropic 2 1 1 '2D 1H-1H TOCSY' 2 isotropic 3 1 1 '2D 1H-1H DQF-COSY' 2 isotropic 4 1 1 '2D 1H-31P HSQC' 3 isotropic 5 1 1 '2D 1H-13C HSQC' 2 isotropic 6 1 1 '2D 1H-15N HSQC' 1 isotropic 7 1 2 '2D 1H-13C HSQC' 2 anisotropic # _pdbx_nmr_refine.entry_id 8ZD7 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details 'RDC was used for refinement' _pdbx_nmr_refine.software_ordinal 3 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'chemical shift assignment' NMRFAM-SPARKY ? 'Lee W, Tonelli M, Markley JL' 2 'structure calculation' CNS ? 'Brunger, Adams, Clore, Gros, Nilges and Read' 3 refinement CNS ? 'Brunger, Adams, Clore, Gros, Nilges and Read' 4 'peak picking' NMRFAM-SPARKY ? 'Lee W, Tonelli M, Markley JL' 5 processing TopSpin ? 'Bruker Biospin' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A1L1R C10 C N N 1 A1L1R C14 C Y N 2 A1L1R C13 C N N 3 A1L1R C12 C N N 4 A1L1R C16 C Y N 5 A1L1R C11 C N N 6 A1L1R N01 N Y N 7 A1L1R C06 C Y N 8 A1L1R C05 C Y N 9 A1L1R C04 C Y N 10 A1L1R C03 C Y N 11 A1L1R C02 C Y N 12 A1L1R N02 N Y N 13 A1L1R C09 C Y N 14 A1L1R C08 C Y N 15 A1L1R C07 C Y N 16 A1L1R C01 C N N 17 A1L1R N03 N N N 18 A1L1R O01 O N N 19 A1L1R N04 N N N 20 A1L1R N05 N N N 21 A1L1R O02 O N N 22 A1L1R N06 N Y N 23 A1L1R C18 C Y N 24 A1L1R C17 C Y N 25 A1L1R C15 C Y N 26 A1L1R N07 N Y N 27 A1L1R C21 C Y N 28 A1L1R C20 C Y N 29 A1L1R C19 C Y N 30 A1L1R C22 C N N 31 A1L1R H11 H N N 32 A1L1R H12 H N N 33 A1L1R H15 H N N 34 A1L1R H08 H N N 35 A1L1R H07 H N N 36 A1L1R H03 H N N 37 A1L1R H02 H N N 38 A1L1R H05 H N N 39 A1L1R H04 H N N 40 A1L1R H32 H N N 41 A1L1R H31 H N N 42 A1L1R H33 H N N 43 A1L1R H06 H N N 44 A1L1R H09 H N N 45 A1L1R H13 H N N 46 A1L1R H14 H N N 47 A1L1R H17 H N N 48 A1L1R H16 H N N 49 A1L1R H42 H N N 50 A1L1R H41 H N N 51 A1L1R H43 H N N 52 DA OP3 O N N 53 DA P P N N 54 DA OP1 O N N 55 DA OP2 O N N 56 DA "O5'" O N N 57 DA "C5'" C N N 58 DA "C4'" C N R 59 DA "O4'" O N N 60 DA "C3'" C N S 61 DA "O3'" O N N 62 DA "C2'" C N N 63 DA "C1'" C N R 64 DA N9 N Y N 65 DA C8 C Y N 66 DA N7 N Y N 67 DA C5 C Y N 68 DA C6 C Y N 69 DA N6 N N N 70 DA N1 N Y N 71 DA C2 C Y N 72 DA N3 N Y N 73 DA C4 C Y N 74 DA HOP3 H N N 75 DA HOP2 H N N 76 DA "H5'" H N N 77 DA "H5''" H N N 78 DA "H4'" H N N 79 DA "H3'" H N N 80 DA "HO3'" H N N 81 DA "H2'" H N N 82 DA "H2''" H N N 83 DA "H1'" H N N 84 DA H8 H N N 85 DA H61 H N N 86 DA H62 H N N 87 DA H2 H N N 88 DC OP3 O N N 89 DC P P N N 90 DC OP1 O N N 91 DC OP2 O N N 92 DC "O5'" O N N 93 DC "C5'" C N N 94 DC "C4'" C N R 95 DC "O4'" O N N 96 DC "C3'" C N S 97 DC "O3'" O N N 98 DC "C2'" C N N 99 DC "C1'" C N R 100 DC N1 N N N 101 DC C2 C N N 102 DC O2 O N N 103 DC N3 N N N 104 DC C4 C N N 105 DC N4 N N N 106 DC C5 C N N 107 DC C6 C N N 108 DC HOP3 H N N 109 DC HOP2 H N N 110 DC "H5'" H N N 111 DC "H5''" H N N 112 DC "H4'" H N N 113 DC "H3'" H N N 114 DC "HO3'" H N N 115 DC "H2'" H N N 116 DC "H2''" H N N 117 DC "H1'" H N N 118 DC H41 H N N 119 DC H42 H N N 120 DC H5 H N N 121 DC H6 H N N 122 DG OP3 O N N 123 DG P P N N 124 DG OP1 O N N 125 DG OP2 O N N 126 DG "O5'" O N N 127 DG "C5'" C N N 128 DG "C4'" C N R 129 DG "O4'" O N N 130 DG "C3'" C N S 131 DG "O3'" O N N 132 DG "C2'" C N N 133 DG "C1'" C N R 134 DG N9 N Y N 135 DG C8 C Y N 136 DG N7 N Y N 137 DG C5 C Y N 138 DG C6 C N N 139 DG O6 O N N 140 DG N1 N N N 141 DG C2 C N N 142 DG N2 N N N 143 DG N3 N N N 144 DG C4 C Y N 145 DG HOP3 H N N 146 DG HOP2 H N N 147 DG "H5'" H N N 148 DG "H5''" H N N 149 DG "H4'" H N N 150 DG "H3'" H N N 151 DG "HO3'" H N N 152 DG "H2'" H N N 153 DG "H2''" H N N 154 DG "H1'" H N N 155 DG H8 H N N 156 DG H1 H N N 157 DG H21 H N N 158 DG H22 H N N 159 DT OP3 O N N 160 DT P P N N 161 DT OP1 O N N 162 DT OP2 O N N 163 DT "O5'" O N N 164 DT "C5'" C N N 165 DT "C4'" C N R 166 DT "O4'" O N N 167 DT "C3'" C N S 168 DT "O3'" O N N 169 DT "C2'" C N N 170 DT "C1'" C N R 171 DT N1 N N N 172 DT C2 C N N 173 DT O2 O N N 174 DT N3 N N N 175 DT C4 C N N 176 DT O4 O N N 177 DT C5 C N N 178 DT C7 C N N 179 DT C6 C N N 180 DT HOP3 H N N 181 DT HOP2 H N N 182 DT "H5'" H N N 183 DT "H5''" H N N 184 DT "H4'" H N N 185 DT "H3'" H N N 186 DT "HO3'" H N N 187 DT "H2'" H N N 188 DT "H2''" H N N 189 DT "H1'" H N N 190 DT H3 H N N 191 DT H71 H N N 192 DT H72 H N N 193 DT H73 H N N 194 DT H6 H N N 195 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A1L1R C22 C21 sing N N 1 A1L1R C20 C21 doub Y N 2 A1L1R C20 C19 sing Y N 3 A1L1R C21 N07 sing Y N 4 A1L1R C19 C17 doub Y N 5 A1L1R N07 C18 doub Y N 6 A1L1R C17 C18 sing Y N 7 A1L1R C17 C16 sing Y N 8 A1L1R C18 N06 sing Y N 9 A1L1R C01 C02 sing N N 10 A1L1R C16 C15 doub Y N 11 A1L1R N06 C14 doub Y N 12 A1L1R C02 N01 sing Y N 13 A1L1R C02 C03 doub Y N 14 A1L1R C15 C14 sing Y N 15 A1L1R N01 C06 doub Y N 16 A1L1R C14 N05 sing N N 17 A1L1R C03 C04 sing Y N 18 A1L1R N05 C13 sing N N 19 A1L1R C06 N02 sing Y N 20 A1L1R C06 C05 sing Y N 21 A1L1R C04 C05 doub Y N 22 A1L1R N02 C09 doub Y N 23 A1L1R C05 C07 sing Y N 24 A1L1R C13 O02 doub N N 25 A1L1R C13 C12 sing N N 26 A1L1R C09 N03 sing N N 27 A1L1R C09 C08 sing Y N 28 A1L1R C07 C08 doub Y N 29 A1L1R N03 C10 sing N N 30 A1L1R C12 N04 sing N N 31 A1L1R C11 C10 sing N N 32 A1L1R C11 N04 sing N N 33 A1L1R C10 O01 doub N N 34 A1L1R C12 H11 sing N N 35 A1L1R C12 H12 sing N N 36 A1L1R C16 H15 sing N N 37 A1L1R C11 H08 sing N N 38 A1L1R C11 H07 sing N N 39 A1L1R C04 H03 sing N N 40 A1L1R C03 H02 sing N N 41 A1L1R C08 H05 sing N N 42 A1L1R C07 H04 sing N N 43 A1L1R C01 H32 sing N N 44 A1L1R C01 H31 sing N N 45 A1L1R C01 H33 sing N N 46 A1L1R N03 H06 sing N N 47 A1L1R N04 H09 sing N N 48 A1L1R N05 H13 sing N N 49 A1L1R C15 H14 sing N N 50 A1L1R C20 H17 sing N N 51 A1L1R C19 H16 sing N N 52 A1L1R C22 H42 sing N N 53 A1L1R C22 H41 sing N N 54 A1L1R C22 H43 sing N N 55 DA OP3 P sing N N 56 DA OP3 HOP3 sing N N 57 DA P OP1 doub N N 58 DA P OP2 sing N N 59 DA P "O5'" sing N N 60 DA OP2 HOP2 sing N N 61 DA "O5'" "C5'" sing N N 62 DA "C5'" "C4'" sing N N 63 DA "C5'" "H5'" sing N N 64 DA "C5'" "H5''" sing N N 65 DA "C4'" "O4'" sing N N 66 DA "C4'" "C3'" sing N N 67 DA "C4'" "H4'" sing N N 68 DA "O4'" "C1'" sing N N 69 DA "C3'" "O3'" sing N N 70 DA "C3'" "C2'" sing N N 71 DA "C3'" "H3'" sing N N 72 DA "O3'" "HO3'" sing N N 73 DA "C2'" "C1'" sing N N 74 DA "C2'" "H2'" sing N N 75 DA "C2'" "H2''" sing N N 76 DA "C1'" N9 sing N N 77 DA "C1'" "H1'" sing N N 78 DA N9 C8 sing Y N 79 DA N9 C4 sing Y N 80 DA C8 N7 doub Y N 81 DA C8 H8 sing N N 82 DA N7 C5 sing Y N 83 DA C5 C6 sing Y N 84 DA C5 C4 doub Y N 85 DA C6 N6 sing N N 86 DA C6 N1 doub Y N 87 DA N6 H61 sing N N 88 DA N6 H62 sing N N 89 DA N1 C2 sing Y N 90 DA C2 N3 doub Y N 91 DA C2 H2 sing N N 92 DA N3 C4 sing Y N 93 DC OP3 P sing N N 94 DC OP3 HOP3 sing N N 95 DC P OP1 doub N N 96 DC P OP2 sing N N 97 DC P "O5'" sing N N 98 DC OP2 HOP2 sing N N 99 DC "O5'" "C5'" sing N N 100 DC "C5'" "C4'" sing N N 101 DC "C5'" "H5'" sing N N 102 DC "C5'" "H5''" sing N N 103 DC "C4'" "O4'" sing N N 104 DC "C4'" "C3'" sing N N 105 DC "C4'" "H4'" sing N N 106 DC "O4'" "C1'" sing N N 107 DC "C3'" "O3'" sing N N 108 DC "C3'" "C2'" sing N N 109 DC "C3'" "H3'" sing N N 110 DC "O3'" "HO3'" sing N N 111 DC "C2'" "C1'" sing N N 112 DC "C2'" "H2'" sing N N 113 DC "C2'" "H2''" sing N N 114 DC "C1'" N1 sing N N 115 DC "C1'" "H1'" sing N N 116 DC N1 C2 sing N N 117 DC N1 C6 sing N N 118 DC C2 O2 doub N N 119 DC C2 N3 sing N N 120 DC N3 C4 doub N N 121 DC C4 N4 sing N N 122 DC C4 C5 sing N N 123 DC N4 H41 sing N N 124 DC N4 H42 sing N N 125 DC C5 C6 doub N N 126 DC C5 H5 sing N N 127 DC C6 H6 sing N N 128 DG OP3 P sing N N 129 DG OP3 HOP3 sing N N 130 DG P OP1 doub N N 131 DG P OP2 sing N N 132 DG P "O5'" sing N N 133 DG OP2 HOP2 sing N N 134 DG "O5'" "C5'" sing N N 135 DG "C5'" "C4'" sing N N 136 DG "C5'" "H5'" sing N N 137 DG "C5'" "H5''" sing N N 138 DG "C4'" "O4'" sing N N 139 DG "C4'" "C3'" sing N N 140 DG "C4'" "H4'" sing N N 141 DG "O4'" "C1'" sing N N 142 DG "C3'" "O3'" sing N N 143 DG "C3'" "C2'" sing N N 144 DG "C3'" "H3'" sing N N 145 DG "O3'" "HO3'" sing N N 146 DG "C2'" "C1'" sing N N 147 DG "C2'" "H2'" sing N N 148 DG "C2'" "H2''" sing N N 149 DG "C1'" N9 sing N N 150 DG "C1'" "H1'" sing N N 151 DG N9 C8 sing Y N 152 DG N9 C4 sing Y N 153 DG C8 N7 doub Y N 154 DG C8 H8 sing N N 155 DG N7 C5 sing Y N 156 DG C5 C6 sing N N 157 DG C5 C4 doub Y N 158 DG C6 O6 doub N N 159 DG C6 N1 sing N N 160 DG N1 C2 sing N N 161 DG N1 H1 sing N N 162 DG C2 N2 sing N N 163 DG C2 N3 doub N N 164 DG N2 H21 sing N N 165 DG N2 H22 sing N N 166 DG N3 C4 sing N N 167 DT OP3 P sing N N 168 DT OP3 HOP3 sing N N 169 DT P OP1 doub N N 170 DT P OP2 sing N N 171 DT P "O5'" sing N N 172 DT OP2 HOP2 sing N N 173 DT "O5'" "C5'" sing N N 174 DT "C5'" "C4'" sing N N 175 DT "C5'" "H5'" sing N N 176 DT "C5'" "H5''" sing N N 177 DT "C4'" "O4'" sing N N 178 DT "C4'" "C3'" sing N N 179 DT "C4'" "H4'" sing N N 180 DT "O4'" "C1'" sing N N 181 DT "C3'" "O3'" sing N N 182 DT "C3'" "C2'" sing N N 183 DT "C3'" "H3'" sing N N 184 DT "O3'" "HO3'" sing N N 185 DT "C2'" "C1'" sing N N 186 DT "C2'" "H2'" sing N N 187 DT "C2'" "H2''" sing N N 188 DT "C1'" N1 sing N N 189 DT "C1'" "H1'" sing N N 190 DT N1 C2 sing N N 191 DT N1 C6 sing N N 192 DT C2 O2 doub N N 193 DT C2 N3 sing N N 194 DT N3 C4 sing N N 195 DT N3 H3 sing N N 196 DT C4 O4 doub N N 197 DT C4 C5 sing N N 198 DT C5 C7 sing N N 199 DT C5 C6 doub N N 200 DT C7 H71 sing N N 201 DT C7 H72 sing N N 202 DT C7 H73 sing N N 203 DT C6 H6 sing N N 204 # _ndb_struct_conf_na.entry_id 8ZD7 _ndb_struct_conf_na.feature 'double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 11 1_555 0.094 -0.156 -0.050 -0.012 1.872 1.510 1 1_DC1:DG22_2 1 1 ? 2 22 ? 19 1 1 A DT 2 1_555 B DA 10 1_555 0.055 -0.205 0.102 -0.825 -1.866 -3.701 2 1_DT2:DA21_2 1 2 ? 2 21 ? 20 1 1 A DA 3 1_555 B DT 9 1_555 -0.113 -0.171 0.097 -0.832 -0.653 -2.707 3 1_DA3:DT20_2 1 3 ? 2 20 ? 20 1 1 A DA 4 1_555 B DT 8 1_555 0.080 -0.131 0.136 -0.209 -2.906 -1.102 4 1_DA4:DT19_2 1 4 ? 2 19 ? 20 1 1 A DC 5 1_555 B DG 7 1_555 0.729 -0.235 0.204 -3.093 -0.858 4.464 5 1_DC5:DG18_2 1 5 ? 2 18 ? 19 1 1 A DG 7 1_555 B DC 5 1_555 -0.183 -0.241 0.134 1.890 -0.501 0.525 6 1_DG7:DC16_2 1 7 ? 2 16 ? 19 1 1 A DA 8 1_555 B DT 4 1_555 -0.293 -0.196 0.174 2.251 -0.170 -5.443 7 1_DA8:DT15_2 1 8 ? 2 15 ? 20 1 1 A DA 9 1_555 B DT 3 1_555 -0.286 -0.208 0.149 1.926 0.566 -7.210 8 1_DA9:DT14_2 1 9 ? 2 14 ? 20 1 1 A DT 10 1_555 B DA 2 1_555 0.485 -0.263 0.105 -0.784 -0.661 -11.619 9 1_DT10:DA13_2 1 10 ? 2 13 ? 20 1 1 A DG 11 1_555 B DC 1 1_555 -0.010 -0.185 -0.029 -1.437 0.384 -3.404 10 1_DG11:DC12_2 1 11 ? 2 12 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 11 1_555 A DT 2 1_555 B DA 10 1_555 -0.512 -0.593 3.716 2.048 -9.575 37.944 0.441 1.048 3.720 -14.435 -3.087 39.142 1 11_DC1DT2:DA21DG22_22 1 1 ? 2 22 ? 1 2 ? 2 21 ? 1 A DT 2 1_555 B DA 10 1_555 A DA 3 1_555 B DT 9 1_555 0.177 -0.881 3.173 0.566 0.500 36.211 -1.486 -0.208 3.163 0.805 -0.911 36.219 2 11_DT2DA3:DT20DA21_22 1 2 ? 2 21 ? 1 3 ? 2 20 ? 1 A DA 3 1_555 B DT 9 1_555 A DA 4 1_555 B DT 8 1_555 0.163 -0.708 3.228 0.610 -3.053 38.440 -0.696 -0.172 3.274 -4.627 -0.925 38.561 3 11_DA3DA4:DT19DT20_22 1 3 ? 2 20 ? 1 4 ? 2 19 ? 1 A DA 4 1_555 B DT 8 1_555 A DC 5 1_555 B DG 7 1_555 0.237 -0.686 3.250 -0.125 3.643 38.630 -1.470 -0.371 3.174 5.492 0.188 38.795 4 11_DA4DC5:DG18DT19_22 1 4 ? 2 19 ? 1 5 ? 2 18 ? 1 A DG 7 1_555 B DC 5 1_555 A DA 8 1_555 B DT 4 1_555 -0.411 0.327 3.601 -1.366 1.958 40.271 0.230 0.426 3.623 2.841 1.982 40.339 5 11_DG7DA8:DT15DC16_22 1 7 ? 2 16 ? 1 8 ? 2 15 ? 1 A DA 8 1_555 B DT 4 1_555 A DA 9 1_555 B DT 3 1_555 -0.188 -0.644 3.285 -0.805 0.433 37.874 -1.047 0.186 3.281 0.667 1.240 37.885 6 11_DA8DA9:DT14DT15_22 1 8 ? 2 15 ? 1 9 ? 2 14 ? 1 A DA 9 1_555 B DT 3 1_555 A DT 10 1_555 B DA 2 1_555 -0.197 -0.454 3.420 0.347 2.592 40.859 -0.945 0.321 3.384 3.709 -0.497 40.939 7 11_DA9DT10:DA13DT14_22 1 9 ? 2 14 ? 1 10 ? 2 13 ? 1 A DT 10 1_555 B DA 2 1_555 A DG 11 1_555 B DC 1 1_555 0.488 -0.974 3.308 1.116 -3.116 34.668 -1.141 -0.641 3.394 -5.214 -1.868 34.820 8 11_DT10DG11:DC12DA13_22 1 10 ? 2 13 ? 1 11 ? 2 12 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Japan Society for the Promotion of Science (JSPS)' Japan JP22H05536 1 'Japan Society for the Promotion of Science (JSPS)' Japan JP23J02416 2 'Japan Agency for Medical Research and Development (AMED)' Japan JP23ama121001 3 'Japan Science and Technology' Japan JPMJFS2125 4 'Japan Society for the Promotion of Science (JSPS)' Japan JP21K06047 5 # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 'AVANCE III' ? Bruker 950 ? 2 'AVANCE III HD' ? Bruker 800 ? 3 'AVANCE III HD' ? Bruker 600 ? 4 'AVANCE III HD' ? Bruker 500 ? # _atom_sites.entry_id 8ZD7 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _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 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C H N O P # loop_ #