data_8ZD2 # _entry.id 8ZD2 # _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 8ZD2 pdb_00008zd2 10.2210/pdb8zd2/pdb WWPDB D_1300046409 ? ? BMRB 36662 ? 10.13018/BMR36662 # 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' 3 2 'Structure model' 'Derived calculations' # 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 4 2 'Structure model' ndb_struct_na_base_pair 5 2 'Structure model' ndb_struct_na_base_pair_step # 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' 13 2 'Structure model' '_ndb_struct_na_base_pair.buckle' 14 2 'Structure model' '_ndb_struct_na_base_pair.opening' 15 2 'Structure model' '_ndb_struct_na_base_pair.propeller' 16 2 'Structure model' '_ndb_struct_na_base_pair.shear' 17 2 'Structure model' '_ndb_struct_na_base_pair.stagger' 18 2 'Structure model' '_ndb_struct_na_base_pair.stretch' 19 2 'Structure model' '_ndb_struct_na_base_pair_step.helical_rise' 20 2 'Structure model' '_ndb_struct_na_base_pair_step.helical_twist' 21 2 'Structure model' '_ndb_struct_na_base_pair_step.inclination' 22 2 'Structure model' '_ndb_struct_na_base_pair_step.rise' 23 2 'Structure model' '_ndb_struct_na_base_pair_step.roll' 24 2 'Structure model' '_ndb_struct_na_base_pair_step.shift' 25 2 'Structure model' '_ndb_struct_na_base_pair_step.slide' 26 2 'Structure model' '_ndb_struct_na_base_pair_step.tilt' 27 2 'Structure model' '_ndb_struct_na_base_pair_step.tip' 28 2 'Structure model' '_ndb_struct_na_base_pair_step.twist' 29 2 'Structure model' '_ndb_struct_na_base_pair_step.x_displacement' 30 2 'Structure model' '_ndb_struct_na_base_pair_step.y_displacement' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr . _pdbx_database_status.entry_id 8ZD2 _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 # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'NMR structure of the (CGG-dsDNA:ND=) 1:2 complex' _pdbx_database_related.db_id 36662 _pdbx_database_related.content_type 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 ? 'Furuita, K.' 2 ? 'Yamada, T.' 3 ? 'Nomura, M.' 4 ? 'Nakatani, K.' 5 ? 'Kojima, C.' 6 ? # _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)-3-[[3-[(7-methyl-1,8-naphthyridin-2-yl)amino]-3-oxidanylidene-propyl]amino]propanamide' 443.501 2 ? ? ? ? # 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)-3-[[3-[(7-methyl-1,8-naphthyridin-2-yl)amino]-3-oxidanylidene-propyl]amino]propanamide' _pdbx_entity_nonpoly.comp_id A1L1S # 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 A1L1S non-polymer . '~{N}-(7-methyl-1,8-naphthyridin-2-yl)-3-[[3-[(7-methyl-1,8-naphthyridin-2-yl)amino]-3-oxidanylidene-propyl]amino]propanamide' ? 'C24 H25 N7 O2' 443.501 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 A1L1S _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id A1L1S _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 ? # 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 C 3 A1L1S 1 101 24 A1L1S MOL 1 . D 3 A1L1S 1 101 23 A1L1S MOL 2 . # _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 8ZD2 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 8ZD2 _struct.title 'NMR structure of the (CGG-dsDNA:ND=) 1:2 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 8ZD2 _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 ? D 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 8ZD2 8ZD2 ? 1 ? 1 2 PDB 8ZD2 8ZD2 ? 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 8ZD2 1 1 ? 11 ? 8ZD2 1 ? 11 ? 1 11 2 2 8ZD2 2 1 ? 11 ? 8ZD2 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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1540 ? 1 MORE -1 ? 1 'SSA (A^2)' 4620 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 DA 8 N1 ? ? ? 1_555 B DT 4 N3 ? ? 1 DA 8 2 DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 4 O4 ? ? 1 DA 8 2 DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 3 N3 ? ? 1 DA 9 2 DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 3 O4 ? ? 1 DA 9 2 DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 2 N1 ? ? 1 DT 10 2 DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 2 N6 ? ? 1 DT 10 2 DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? ? 1 DG 11 2 DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? ? 1 DG 11 2 DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 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 8ZD2 _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 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 2 1 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 3 1 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 4 2 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.51 5 2 H62 1 DA 9 ? ? O4 2 DT 14 ? ? 1.58 6 2 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 7 2 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 8 3 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 9 3 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 10 4 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.51 11 4 H62 1 DA 9 ? ? O4 2 DT 14 ? ? 1.58 12 4 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.60 13 5 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.56 14 5 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 15 6 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 16 6 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 17 7 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 18 7 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 19 8 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.52 20 8 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 21 8 H62 1 DA 9 ? ? O4 2 DT 14 ? ? 1.59 22 9 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 23 9 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 24 9 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.60 25 10 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.52 26 10 H62 1 DA 9 ? ? O4 2 DT 14 ? ? 1.58 27 10 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 28 11 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 29 12 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.50 30 12 H62 1 DA 9 ? ? O4 2 DT 14 ? ? 1.58 31 12 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 32 12 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 33 13 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.52 34 13 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.58 35 13 H62 1 DA 9 ? ? O4 2 DT 14 ? ? 1.59 36 13 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 37 14 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 38 14 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 39 15 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 40 15 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 41 15 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.60 42 16 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 43 16 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 44 16 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 45 16 H62 1 DA 9 ? ? O4 2 DT 14 ? ? 1.60 46 17 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 47 17 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 48 17 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.60 49 18 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 50 18 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.60 51 19 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.56 52 20 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 53 20 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 54 21 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 55 21 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 56 22 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 57 23 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 58 23 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 59 24 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 60 24 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 61 25 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 62 25 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 63 26 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 64 26 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.57 65 27 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 66 27 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 67 28 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.53 68 28 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.59 69 28 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.60 70 29 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 71 29 H22 2 DG 17 ? ? N07 1 A1L1S 101 ? ? 1.59 72 29 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.60 73 30 O6 1 DG 11 ? ? H42 2 DC 12 ? ? 1.54 74 30 H62 1 DA 3 ? ? O4 2 DT 20 ? ? 1.58 # _pdbx_nmr_ensemble.entry_id 8ZD2 _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 8ZD2 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents ;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'), 4.0 mM None ND, 20 mM None sodium phosphate (pH 6.8), 100 mM None NaCl, 95% H2O/5% D2O ; _pdbx_nmr_sample_details.solvent_system '95% H2O/5% D2O' _pdbx_nmr_sample_details.label CGG-dsDNA-ND _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details ? # 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 ND 4.0 ? mM None 1 'sodium phosphate (pH 6.8)' 20 ? mM None 1 NaCl 100 ? mM None # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.details _pdbx_nmr_exptl_sample_conditions.ionic_strength_err _pdbx_nmr_exptl_sample_conditions.ionic_strength_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_err _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.pressure_err _pdbx_nmr_exptl_sample_conditions.temperature_err _pdbx_nmr_exptl_sample_conditions.temperature_units 1 313 atm 1 6.8 120 'For distance constraints' ? mM condition1 ? pH ? ? K 2 313 atm 1 6.8 120 ;For RDC restraints containing 10 mg/mL of pf1 ; ? mM condition2 ? pH ? ? 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' 1 isotropic 6 1 1 '2D 1H-15N HSQC' 1 isotropic 7 2 1 '2D 1H-13C HSQC' 1 anisotropic # _pdbx_nmr_refine.entry_id 8ZD2 _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 A1L1S O02 O N N 1 A1L1S C15 C N N 2 A1L1S N05 N N N 3 A1L1S C16 C Y N 4 A1L1S C17 C Y N 5 A1L1S C18 C Y N 6 A1L1S C19 C Y N 7 A1L1S C21 C Y N 8 A1L1S C22 C Y N 9 A1L1S C23 C Y N 10 A1L1S C24 C N N 11 A1L1S N07 N Y N 12 A1L1S C20 C Y N 13 A1L1S N06 N Y N 14 A1L1S C14 C N N 15 A1L1S C13 C N N 16 A1L1S N04 N N N 17 A1L1S C12 C N N 18 A1L1S C11 C N N 19 A1L1S C10 C N N 20 A1L1S O01 O N N 21 A1L1S N03 N N N 22 A1L1S C09 C Y N 23 A1L1S C08 C Y N 24 A1L1S C07 C Y N 25 A1L1S C05 C Y N 26 A1L1S C06 C Y N 27 A1L1S N02 N Y N 28 A1L1S C04 C Y N 29 A1L1S C03 C Y N 30 A1L1S C02 C Y N 31 A1L1S N01 N Y N 32 A1L1S C01 C N N 33 A1L1S H15 H N N 34 A1L1S H16 H N N 35 A1L1S H17 H N N 36 A1L1S H18 H N N 37 A1L1S H19 H N N 38 A1L1S H43 H N N 39 A1L1S H41 H N N 40 A1L1S H42 H N N 41 A1L1S H14 H N N 42 A1L1S H13 H N N 43 A1L1S H12 H N N 44 A1L1S H11 H N N 45 A1L1S H20 H N N 46 A1L1S H09 H N N 47 A1L1S H10 H N N 48 A1L1S H07 H N N 49 A1L1S H08 H N N 50 A1L1S H06 H N N 51 A1L1S H05 H N N 52 A1L1S H04 H N N 53 A1L1S H03 H N N 54 A1L1S H02 H N N 55 A1L1S H31 H N N 56 A1L1S H32 H N N 57 A1L1S H33 H N N 58 DA OP3 O N N 59 DA P P N N 60 DA OP1 O N N 61 DA OP2 O N N 62 DA "O5'" O N N 63 DA "C5'" C N N 64 DA "C4'" C N R 65 DA "O4'" O N N 66 DA "C3'" C N S 67 DA "O3'" O N N 68 DA "C2'" C N N 69 DA "C1'" C N R 70 DA N9 N Y N 71 DA C8 C Y N 72 DA N7 N Y N 73 DA C5 C Y N 74 DA C6 C Y N 75 DA N6 N N N 76 DA N1 N Y N 77 DA C2 C Y N 78 DA N3 N Y N 79 DA C4 C Y N 80 DA HOP3 H N N 81 DA HOP2 H N N 82 DA "H5'" H N N 83 DA "H5''" H N N 84 DA "H4'" H N N 85 DA "H3'" H N N 86 DA "HO3'" H N N 87 DA "H2'" H N N 88 DA "H2''" H N N 89 DA "H1'" H N N 90 DA H8 H N N 91 DA H61 H N N 92 DA H62 H N N 93 DA H2 H N N 94 DC OP3 O N N 95 DC P P N N 96 DC OP1 O N N 97 DC OP2 O N N 98 DC "O5'" O N N 99 DC "C5'" C N N 100 DC "C4'" C N R 101 DC "O4'" O N N 102 DC "C3'" C N S 103 DC "O3'" O N N 104 DC "C2'" C N N 105 DC "C1'" C N R 106 DC N1 N N N 107 DC C2 C N N 108 DC O2 O N N 109 DC N3 N N N 110 DC C4 C N N 111 DC N4 N N N 112 DC C5 C N N 113 DC C6 C N N 114 DC HOP3 H N N 115 DC HOP2 H N N 116 DC "H5'" H N N 117 DC "H5''" H N N 118 DC "H4'" H N N 119 DC "H3'" H N N 120 DC "HO3'" H N N 121 DC "H2'" H N N 122 DC "H2''" H N N 123 DC "H1'" H N N 124 DC H41 H N N 125 DC H42 H N N 126 DC H5 H N N 127 DC H6 H N N 128 DG OP3 O N N 129 DG P P N N 130 DG OP1 O N N 131 DG OP2 O N N 132 DG "O5'" O N N 133 DG "C5'" C N N 134 DG "C4'" C N R 135 DG "O4'" O N N 136 DG "C3'" C N S 137 DG "O3'" O N N 138 DG "C2'" C N N 139 DG "C1'" C N R 140 DG N9 N Y N 141 DG C8 C Y N 142 DG N7 N Y N 143 DG C5 C Y N 144 DG C6 C N N 145 DG O6 O N N 146 DG N1 N N N 147 DG C2 C N N 148 DG N2 N N N 149 DG N3 N N N 150 DG C4 C Y N 151 DG HOP3 H N N 152 DG HOP2 H N N 153 DG "H5'" H N N 154 DG "H5''" H N N 155 DG "H4'" H N N 156 DG "H3'" H N N 157 DG "HO3'" H N N 158 DG "H2'" H N N 159 DG "H2''" H N N 160 DG "H1'" H N N 161 DG H8 H N N 162 DG H1 H N N 163 DG H21 H N N 164 DG H22 H N N 165 DT OP3 O N N 166 DT P P N N 167 DT OP1 O N N 168 DT OP2 O N N 169 DT "O5'" O N N 170 DT "C5'" C N N 171 DT "C4'" C N R 172 DT "O4'" O N N 173 DT "C3'" C N S 174 DT "O3'" O N N 175 DT "C2'" C N N 176 DT "C1'" C N R 177 DT N1 N N N 178 DT C2 C N N 179 DT O2 O N N 180 DT N3 N N N 181 DT C4 C N N 182 DT O4 O N N 183 DT C5 C N N 184 DT C7 C N N 185 DT C6 C N N 186 DT HOP3 H N N 187 DT HOP2 H N N 188 DT "H5'" H N N 189 DT "H5''" H N N 190 DT "H4'" H N N 191 DT "H3'" H N N 192 DT "HO3'" H N N 193 DT "H2'" H N N 194 DT "H2''" H N N 195 DT "H1'" H N N 196 DT H3 H N N 197 DT H71 H N N 198 DT H72 H N N 199 DT H73 H N N 200 DT H6 H N N 201 # 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 A1L1S C01 C02 sing N N 1 A1L1S C03 C02 doub Y N 2 A1L1S C03 C04 sing Y N 3 A1L1S C02 N01 sing Y N 4 A1L1S C04 C05 doub Y N 5 A1L1S N01 C06 doub Y N 6 A1L1S C05 C06 sing Y N 7 A1L1S C05 C07 sing Y N 8 A1L1S C06 N02 sing Y N 9 A1L1S C07 C08 doub Y N 10 A1L1S N02 C09 doub Y N 11 A1L1S C08 C09 sing Y N 12 A1L1S C09 N03 sing N N 13 A1L1S C24 C23 sing N N 14 A1L1S N03 C10 sing N N 15 A1L1S C23 C22 sing Y N 16 A1L1S C23 N07 doub Y N 17 A1L1S C22 C21 doub Y N 18 A1L1S N07 C20 sing Y N 19 A1L1S C10 O01 doub N N 20 A1L1S C10 C11 sing N N 21 A1L1S C21 C19 sing Y N 22 A1L1S C20 C19 doub Y N 23 A1L1S C20 N06 sing Y N 24 A1L1S C11 C12 sing N N 25 A1L1S C19 C18 sing Y N 26 A1L1S N06 C16 doub Y N 27 A1L1S C16 N05 sing N N 28 A1L1S C16 C17 sing Y N 29 A1L1S C12 N04 sing N N 30 A1L1S C18 C17 doub Y N 31 A1L1S N05 C15 sing N N 32 A1L1S N04 C13 sing N N 33 A1L1S C14 C15 sing N N 34 A1L1S C14 C13 sing N N 35 A1L1S C15 O02 doub N N 36 A1L1S N05 H15 sing N N 37 A1L1S C17 H16 sing N N 38 A1L1S C18 H17 sing N N 39 A1L1S C21 H18 sing N N 40 A1L1S C22 H19 sing N N 41 A1L1S C24 H43 sing N N 42 A1L1S C24 H41 sing N N 43 A1L1S C24 H42 sing N N 44 A1L1S C14 H14 sing N N 45 A1L1S C14 H13 sing N N 46 A1L1S C13 H12 sing N N 47 A1L1S C13 H11 sing N N 48 A1L1S N04 H20 sing N N 49 A1L1S C12 H09 sing N N 50 A1L1S C12 H10 sing N N 51 A1L1S C11 H07 sing N N 52 A1L1S C11 H08 sing N N 53 A1L1S N03 H06 sing N N 54 A1L1S C08 H05 sing N N 55 A1L1S C07 H04 sing N N 56 A1L1S C04 H03 sing N N 57 A1L1S C03 H02 sing N N 58 A1L1S C01 H31 sing N N 59 A1L1S C01 H32 sing N N 60 A1L1S C01 H33 sing N N 61 DA OP3 P sing N N 62 DA OP3 HOP3 sing N N 63 DA P OP1 doub N N 64 DA P OP2 sing N N 65 DA P "O5'" sing N N 66 DA OP2 HOP2 sing N N 67 DA "O5'" "C5'" sing N N 68 DA "C5'" "C4'" sing N N 69 DA "C5'" "H5'" sing N N 70 DA "C5'" "H5''" sing N N 71 DA "C4'" "O4'" sing N N 72 DA "C4'" "C3'" sing N N 73 DA "C4'" "H4'" sing N N 74 DA "O4'" "C1'" sing N N 75 DA "C3'" "O3'" sing N N 76 DA "C3'" "C2'" sing N N 77 DA "C3'" "H3'" sing N N 78 DA "O3'" "HO3'" sing N N 79 DA "C2'" "C1'" sing N N 80 DA "C2'" "H2'" sing N N 81 DA "C2'" "H2''" sing N N 82 DA "C1'" N9 sing N N 83 DA "C1'" "H1'" sing N N 84 DA N9 C8 sing Y N 85 DA N9 C4 sing Y N 86 DA C8 N7 doub Y N 87 DA C8 H8 sing N N 88 DA N7 C5 sing Y N 89 DA C5 C6 sing Y N 90 DA C5 C4 doub Y N 91 DA C6 N6 sing N N 92 DA C6 N1 doub Y N 93 DA N6 H61 sing N N 94 DA N6 H62 sing N N 95 DA N1 C2 sing Y N 96 DA C2 N3 doub Y N 97 DA C2 H2 sing N N 98 DA N3 C4 sing Y N 99 DC OP3 P sing N N 100 DC OP3 HOP3 sing N N 101 DC P OP1 doub N N 102 DC P OP2 sing N N 103 DC P "O5'" sing N N 104 DC OP2 HOP2 sing N N 105 DC "O5'" "C5'" sing N N 106 DC "C5'" "C4'" sing N N 107 DC "C5'" "H5'" sing N N 108 DC "C5'" "H5''" sing N N 109 DC "C4'" "O4'" sing N N 110 DC "C4'" "C3'" sing N N 111 DC "C4'" "H4'" sing N N 112 DC "O4'" "C1'" sing N N 113 DC "C3'" "O3'" sing N N 114 DC "C3'" "C2'" sing N N 115 DC "C3'" "H3'" sing N N 116 DC "O3'" "HO3'" sing N N 117 DC "C2'" "C1'" sing N N 118 DC "C2'" "H2'" sing N N 119 DC "C2'" "H2''" sing N N 120 DC "C1'" N1 sing N N 121 DC "C1'" "H1'" sing N N 122 DC N1 C2 sing N N 123 DC N1 C6 sing N N 124 DC C2 O2 doub N N 125 DC C2 N3 sing N N 126 DC N3 C4 doub N N 127 DC C4 N4 sing N N 128 DC C4 C5 sing N N 129 DC N4 H41 sing N N 130 DC N4 H42 sing N N 131 DC C5 C6 doub N N 132 DC C5 H5 sing N N 133 DC C6 H6 sing N N 134 DG OP3 P sing N N 135 DG OP3 HOP3 sing N N 136 DG P OP1 doub N N 137 DG P OP2 sing N N 138 DG P "O5'" sing N N 139 DG OP2 HOP2 sing N N 140 DG "O5'" "C5'" sing N N 141 DG "C5'" "C4'" sing N N 142 DG "C5'" "H5'" sing N N 143 DG "C5'" "H5''" sing N N 144 DG "C4'" "O4'" sing N N 145 DG "C4'" "C3'" sing N N 146 DG "C4'" "H4'" sing N N 147 DG "O4'" "C1'" sing N N 148 DG "C3'" "O3'" sing N N 149 DG "C3'" "C2'" sing N N 150 DG "C3'" "H3'" sing N N 151 DG "O3'" "HO3'" sing N N 152 DG "C2'" "C1'" sing N N 153 DG "C2'" "H2'" sing N N 154 DG "C2'" "H2''" sing N N 155 DG "C1'" N9 sing N N 156 DG "C1'" "H1'" sing N N 157 DG N9 C8 sing Y N 158 DG N9 C4 sing Y N 159 DG C8 N7 doub Y N 160 DG C8 H8 sing N N 161 DG N7 C5 sing Y N 162 DG C5 C6 sing N N 163 DG C5 C4 doub Y N 164 DG C6 O6 doub N N 165 DG C6 N1 sing N N 166 DG N1 C2 sing N N 167 DG N1 H1 sing N N 168 DG C2 N2 sing N N 169 DG C2 N3 doub N N 170 DG N2 H21 sing N N 171 DG N2 H22 sing N N 172 DG N3 C4 sing N N 173 DT OP3 P sing N N 174 DT OP3 HOP3 sing N N 175 DT P OP1 doub N N 176 DT P OP2 sing N N 177 DT P "O5'" sing N N 178 DT OP2 HOP2 sing N N 179 DT "O5'" "C5'" sing N N 180 DT "C5'" "C4'" sing N N 181 DT "C5'" "H5'" sing N N 182 DT "C5'" "H5''" sing N N 183 DT "C4'" "O4'" sing N N 184 DT "C4'" "C3'" sing N N 185 DT "C4'" "H4'" sing N N 186 DT "O4'" "C1'" sing N N 187 DT "C3'" "O3'" sing N N 188 DT "C3'" "C2'" sing N N 189 DT "C3'" "H3'" sing N N 190 DT "O3'" "HO3'" sing N N 191 DT "C2'" "C1'" sing N N 192 DT "C2'" "H2'" sing N N 193 DT "C2'" "H2''" sing N N 194 DT "C1'" N1 sing N N 195 DT "C1'" "H1'" sing N N 196 DT N1 C2 sing N N 197 DT N1 C6 sing N N 198 DT C2 O2 doub N N 199 DT C2 N3 sing N N 200 DT N3 C4 sing N N 201 DT N3 H3 sing N N 202 DT C4 O4 doub N N 203 DT C4 C5 sing N N 204 DT C5 C7 sing N N 205 DT C5 C6 doub N N 206 DT C7 H71 sing N N 207 DT C7 H72 sing N N 208 DT C7 H73 sing N N 209 DT C6 H6 sing N N 210 # _ndb_struct_conf_na.entry_id 8ZD2 _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 0.412 -0.301 -0.097 0.241 2.611 -1.128 1 1_DC1:DG22_2 1 1 ? 2 22 ? 19 1 1 A DT 2 1_555 B DA 10 1_555 -0.089 -0.147 0.139 -0.033 0.777 -3.415 2 1_DT2:DA21_2 1 2 ? 2 21 ? 20 1 1 A DA 3 1_555 B DT 9 1_555 -0.386 -0.291 0.205 0.862 -0.859 -11.407 3 1_DA3:DT20_2 1 3 ? 2 20 ? 20 1 1 A DA 4 1_555 B DT 8 1_555 0.524 -0.024 0.065 -0.289 -0.800 -0.263 4 1_DA4:DT19_2 1 4 ? 2 19 ? 20 1 1 A DA 8 1_555 B DT 4 1_555 -0.396 -0.132 0.105 1.338 2.762 -6.131 5 1_DA8:DT15_2 1 8 ? 2 15 ? 20 1 1 A DA 9 1_555 B DT 3 1_555 -0.295 -0.274 0.024 2.695 1.273 -8.251 6 1_DA9:DT14_2 1 9 ? 2 14 ? 20 1 1 A DT 10 1_555 B DA 2 1_555 0.101 -0.097 0.087 0.590 -5.333 5.851 7 1_DT10:DA13_2 1 10 ? 2 13 ? 20 1 1 A DG 11 1_555 B DC 1 1_555 -0.046 -0.321 0.080 -0.309 -2.173 -5.286 8 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 -0.230 -0.405 3.976 0.716 -9.416 36.236 0.894 0.474 3.950 -14.832 -1.128 37.406 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 -0.344 -1.013 3.124 -0.843 4.972 35.444 -2.317 0.446 2.966 8.116 1.376 35.789 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 0.263 -0.481 3.470 -1.304 0.123 41.562 -0.691 -0.517 3.460 0.173 1.837 41.582 3 11_DA3DA4:DT19DT20_22 1 3 ? 2 20 ? 1 4 ? 2 19 ? 1 A DA 8 1_555 B DT 4 1_555 A DA 9 1_555 B DT 3 1_555 -0.258 -0.641 3.408 -1.018 1.995 34.664 -1.391 0.271 3.373 3.345 1.707 34.734 4 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 0.671 -0.538 3.692 1.002 -4.709 38.542 -0.154 -0.870 3.745 -7.100 -1.511 38.830 5 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 -1.135 0.815 3.254 -4.364 6.490 41.209 0.442 1.117 3.436 9.122 6.134 41.913 6 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 8ZD2 _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_ #