data_7KUB # _entry.id 7KUB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 7KUB pdb_00007kub 10.2210/pdb7kub/pdb WWPDB D_1000253160 ? ? BMRB 30816 ? 10.13018/BMR30816 # 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 2022-06-01 2 'Structure model' 1 1 2024-05-15 # _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' 'Data collection' 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' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 2 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_database_2.pdbx_DOI' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 7KUB _pdbx_database_status.recvd_initial_deposition_date 2020-11-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Au1 Domain of VEGF Readthrough Element' _pdbx_database_related.db_id 30816 _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID ;D'Souza, V.M. ; 1 0000-0002-5397-9481 'Wagner, N.O.' 2 0000-0001-8200-3878 'Edwards, J.M.' 3 0000-0001-7123-2472 # _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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Stop codon readthrough in VEGF-A is regulated by complex signals' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wagner, N.O.' 1 ? primary 'Edwards, J.E.' 2 ? primary 'Abramovich, J.' 3 ? primary 'Gupta, P.' 4 ? primary 'Swaminathan, H.' 5 ? primary 'Rouskin, S.' 6 ? primary ;D'Souza, V.M. ; 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'RNA (60-MER)' _entity.formula_weight 19268.506 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code CUGCUCUACCUUCACCAUGCCAAGUGGUCCCAGGCUGCACCCAUGGCAGAAGGAGGGCAG _entity_poly.pdbx_seq_one_letter_code_can CUGCUCUACCUUCACCAUGCCAAGUGGUCCCAGGCUGCACCCAUGGCAGAAGGAGGGCAG _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 C n 1 2 U n 1 3 G n 1 4 C n 1 5 U n 1 6 C n 1 7 U n 1 8 A n 1 9 C n 1 10 C n 1 11 U n 1 12 U n 1 13 C n 1 14 A n 1 15 C n 1 16 C n 1 17 A n 1 18 U n 1 19 G n 1 20 C n 1 21 C n 1 22 A n 1 23 A n 1 24 G n 1 25 U n 1 26 G n 1 27 G n 1 28 U n 1 29 C n 1 30 C n 1 31 C n 1 32 A n 1 33 G n 1 34 G n 1 35 C n 1 36 U n 1 37 G n 1 38 C n 1 39 A n 1 40 C n 1 41 C n 1 42 C n 1 43 A n 1 44 U n 1 45 G n 1 46 G n 1 47 C n 1 48 A n 1 49 G n 1 50 A n 1 51 A n 1 52 G n 1 53 G n 1 54 A n 1 55 G n 1 56 G n 1 57 G n 1 58 C n 1 59 A n 1 60 G 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 60 _pdbx_entity_src_syn.organism_scientific 'Bos taurus' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9913 _pdbx_entity_src_syn.details ? # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 C 1 43 43 C CYT A . n A 1 2 U 2 44 44 U URI A . n A 1 3 G 3 45 45 G GUA A . n A 1 4 C 4 46 46 C CYT A . n A 1 5 U 5 47 47 U URI A . n A 1 6 C 6 48 48 C CYT A . n A 1 7 U 7 49 49 U URI A . n A 1 8 A 8 50 50 A ADE A . n A 1 9 C 9 51 51 C CYT A . n A 1 10 C 10 52 52 C CYT A . n A 1 11 U 11 53 53 U URI A . n A 1 12 U 12 54 54 U URI A . n A 1 13 C 13 55 55 C CYT A . n A 1 14 A 14 56 56 A ADE A . n A 1 15 C 15 57 57 C CYT A . n A 1 16 C 16 58 58 C CYT A . n A 1 17 A 17 59 59 A ADE A . n A 1 18 U 18 60 60 U URI A . n A 1 19 G 19 61 61 G GUA A . n A 1 20 C 20 62 62 C CYT A . n A 1 21 C 21 63 63 C CYT A . n A 1 22 A 22 64 64 A ADE A . n A 1 23 A 23 65 65 A ADE A . n A 1 24 G 24 66 66 G GUA A . n A 1 25 U 25 67 67 U URI A . n A 1 26 G 26 68 68 G GUA A . n A 1 27 G 27 69 69 G GUA A . n A 1 28 U 28 70 70 U URI A . n A 1 29 C 29 71 71 C CYT A . n A 1 30 C 30 72 72 C CYT A . n A 1 31 C 31 73 73 C CYT A . n A 1 32 A 32 74 74 A ADE A . n A 1 33 G 33 75 75 G GUA A . n A 1 34 G 34 76 76 G GUA A . n A 1 35 C 35 77 77 C CYT A . n A 1 36 U 36 78 78 U URI A . n A 1 37 G 37 79 79 G GUA A . n A 1 38 C 38 80 80 C CYT A . n A 1 39 A 39 81 81 A ADE A . n A 1 40 C 40 82 82 C CYT A . n A 1 41 C 41 83 83 C CYT A . n A 1 42 C 42 84 84 C CYT A . n A 1 43 A 43 85 85 A ADE A . n A 1 44 U 44 86 86 U URI A . n A 1 45 G 45 87 87 G GUA A . n A 1 46 G 46 88 88 G GUA A . n A 1 47 C 47 89 89 C CYT A . n A 1 48 A 48 90 90 A ADE A . n A 1 49 G 49 91 91 G GUA A . n A 1 50 A 50 92 92 A ADE A . n A 1 51 A 51 93 93 A ADE A . n A 1 52 G 52 94 94 G GUA A . n A 1 53 G 53 95 95 G GUA A . n A 1 54 A 54 96 96 A ADE A . n A 1 55 G 55 97 97 G GUA A . n A 1 56 G 56 98 98 G GUA A . n A 1 57 G 57 99 99 G GUA A . n A 1 58 C 58 100 100 C CYT A . n A 1 59 A 59 101 101 A ADE A . n A 1 60 G 60 102 102 G GUA A . n # _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 7KUB _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7KUB _struct.title 'Au1 Domain of VEGF Readthrough Element' _struct.pdbx_model_details 'NMR Structure' _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7KUB _struct_keywords.text 'Stop codon readthrough, VEGF mRNA, stem-loop, RNA' _struct_keywords.pdbx_keywords RNA # _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_ref.id 1 _struct_ref.db_name GB _struct_ref.db_code M32976.1 _struct_ref.pdbx_db_accession 163006 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code CUGCUCUACCUUCACCAUGCCAAGUGGUCCCAGGCUGCACCCAUGGCAGAAGGAGGGCAG _struct_ref.pdbx_align_begin 588 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7KUB _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 60 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 163006 _struct_ref_seq.db_align_beg 588 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 647 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 43 _struct_ref_seq.pdbx_auth_seq_align_end 102 # _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 # loop_ _pdbx_struct_assembly_auth_evidence.id _pdbx_struct_assembly_auth_evidence.assembly_id _pdbx_struct_assembly_auth_evidence.experimental_support _pdbx_struct_assembly_auth_evidence.details 1 1 'native gel electrophoresis' ? 2 1 'isothermal titration calorimetry' ? # _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 ? _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_ _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 C 1 N3 ? ? ? 1_555 A G 60 N1 ? ? A C 43 A G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 60 O6 ? ? A C 43 A G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 60 N2 ? ? A C 43 A G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 A A 59 N1 ? ? A U 44 A A 101 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 A A 59 N6 ? ? A U 44 A A 101 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 58 N3 ? ? A G 45 A C 100 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 58 O2 ? ? A G 45 A C 100 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 58 N4 ? ? A G 45 A C 100 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 57 N1 ? ? A C 46 A G 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 57 O6 ? ? A C 46 A G 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 57 N2 ? ? A C 46 A G 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 N3 ? ? ? 1_555 A G 56 O6 ? ? A U 47 A G 98 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog13 hydrog ? ? A U 5 O2 ? ? ? 1_555 A G 56 N1 ? ? A U 47 A G 98 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 55 N1 ? ? A C 48 A G 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 55 O6 ? ? A C 48 A G 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 55 N2 ? ? A C 48 A G 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 54 N1 ? ? A U 49 A A 96 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 54 N6 ? ? A U 49 A A 96 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 8 N1 ? ? ? 1_555 A G 53 N1 ? ? A A 50 A G 95 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog20 hydrog ? ? A A 8 N6 ? ? ? 1_555 A G 53 O6 ? ? A A 50 A G 95 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog21 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 53 N1 ? ? A C 51 A G 95 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 53 O6 ? ? A C 51 A G 95 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 53 N2 ? ? A C 51 A G 95 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 52 N1 ? ? A C 52 A G 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 52 O6 ? ? A C 52 A G 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 52 N2 ? ? A C 52 A G 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 11 O4 ? ? ? 1_555 A C 47 N4 ? ? A U 53 A C 89 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog28 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 51 N1 ? ? A U 53 A A 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 51 N6 ? ? A U 53 A A 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 12 N3 ? ? ? 1_555 A A 50 N1 ? ? A U 54 A A 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 12 O4 ? ? ? 1_555 A A 50 N6 ? ? A U 54 A A 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 49 N1 ? ? A C 55 A G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 49 O6 ? ? A C 55 A G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 49 N2 ? ? A C 55 A G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A A 14 N1 ? ? ? 1_555 A G 46 N1 ? ? A A 56 A G 88 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog36 hydrog ? ? A A 14 N6 ? ? ? 1_555 A G 46 O6 ? ? A A 56 A G 88 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog37 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 46 N1 ? ? A C 57 A G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 46 O6 ? ? A C 57 A G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 46 N2 ? ? A C 57 A G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 45 N1 ? ? A C 58 A G 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 45 O6 ? ? A C 58 A G 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 45 N2 ? ? A C 58 A G 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A A 17 N1 ? ? ? 1_555 A U 44 N3 ? ? A A 59 A U 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A A 17 N6 ? ? ? 1_555 A U 44 O4 ? ? A A 59 A U 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A U 18 N3 ? ? ? 1_555 A A 43 N1 ? ? A U 60 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A U 18 O4 ? ? ? 1_555 A A 43 N6 ? ? A U 60 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 19 N1 ? ? ? 1_555 A C 42 N3 ? ? A G 61 A C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 19 N2 ? ? ? 1_555 A C 42 O2 ? ? A G 61 A C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 19 O6 ? ? ? 1_555 A C 42 N4 ? ? A G 61 A C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 20 N3 ? ? ? 1_555 A C 41 N4 ? ? A C 62 A C 83 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog51 hydrog ? ? A C 21 N4 ? ? ? 1_555 A C 40 N3 ? ? A C 63 A C 82 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog52 hydrog ? ? A A 22 N6 ? ? ? 1_555 A A 39 N1 ? ? A A 64 A A 81 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog53 hydrog ? ? A G 24 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 66 A C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A G 24 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 66 A C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A G 24 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 66 A C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A U 25 N3 ? ? ? 1_555 A G 37 O6 ? ? A U 67 A G 79 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog57 hydrog ? ? A U 25 O2 ? ? ? 1_555 A G 37 N1 ? ? A U 67 A G 79 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog58 hydrog ? ? A G 26 N1 ? ? ? 1_555 A U 36 O2 ? ? A G 68 A U 78 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog59 hydrog ? ? A G 26 O6 ? ? ? 1_555 A U 36 N3 ? ? A G 68 A U 78 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog60 hydrog ? ? A G 27 N1 ? ? ? 1_555 A C 35 N3 ? ? A G 69 A C 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A G 27 N2 ? ? ? 1_555 A C 35 O2 ? ? A G 69 A C 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A G 27 O6 ? ? ? 1_555 A C 35 N4 ? ? A G 69 A C 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A U 28 N3 ? ? ? 1_555 A G 34 O6 ? ? A U 70 A G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog64 hydrog ? ? A U 28 O2 ? ? ? 1_555 A G 34 N1 ? ? A U 70 A G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog65 hydrog ? ? A C 29 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 71 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 29 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 71 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 29 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 71 A G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 30 O2 ? ? ? 1_555 A G 33 N1 ? ? A C 72 A G 75 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog69 hydrog ? ? A C 47 N3 ? ? ? 1_555 A A 51 N6 ? ? A C 89 A A 93 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 2 "C1'" A C 89 ? ? "O4'" A C 89 ? ? "C4'" A C 89 ? ? 105.11 109.70 -4.59 0.70 N 2 2 "C1'" A A 90 ? ? "O4'" A A 90 ? ? "C4'" A A 90 ? ? 104.76 109.70 -4.94 0.70 N 3 6 "C1'" A C 89 ? ? "O4'" A C 89 ? ? "C4'" A C 89 ? ? 105.20 109.70 -4.50 0.70 N 4 7 "C1'" A C 89 ? ? "O4'" A C 89 ? ? "C4'" A C 89 ? ? 105.45 109.70 -4.25 0.70 N 5 8 "C1'" A C 89 ? ? "O4'" A C 89 ? ? "C4'" A C 89 ? ? 104.83 109.70 -4.87 0.70 N 6 9 "C1'" A C 89 ? ? "O4'" A C 89 ? ? "C4'" A C 89 ? ? 105.11 109.70 -4.59 0.70 N 7 10 "C1'" A C 89 ? ? "O4'" A C 89 ? ? "C4'" A C 89 ? ? 104.91 109.70 -4.79 0.70 N # _pdbx_nmr_ensemble.entry_id 7KUB _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _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 7KUB _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # 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 '100 uM RNA (60-MER), 90% H2O/10% D2O' '90% H2O/10% D2O' Full_H2O solution ? 2 '100 uM RNA (60-MER), 100% D2O' '100% D2O' H3H4_D2O solution ? 3 '100 uM RNA (60-MER), 100% D2O' '100% D2O' H2H3_D2O solution ? 4 '100 uM RNA (60-MER), 100% D2O' '100% D2O' H1H2_D2O solution ? 5 '100 uM RNA (60-MER), 100% D2O' '100% D2O' Full_D2O solution ? # 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 'RNA (60-MER)' 100 ? uM . 2 'RNA (60-MER)' 100 ? uM . 3 'RNA (60-MER)' 100 ? uM . 4 'RNA (60-MER)' 100 ? uM . 5 'RNA (60-MER)' 100 ? uM . # 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 1 280 ? ambient 5.6 50 ? ? mM conditions_H2O ? pH ? ? K 2 311 ? ambient 5.6 50 ? ? mM conditions_D2O_1 ? pH ? ? K 3 311 ? ambient 8.0 50 ? ? mM conditions_D2O_2 ? 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' 1 isotropic 2 2 5 '2D 1H-1H NOESY' 1 isotropic 3 3 2 '2D 1H-1H NOESY' 1 isotropic 4 3 3 '2D 1H-1H NOESY' 1 isotropic 5 3 4 '2D 1H-1H NOESY' 1 isotropic # _pdbx_nmr_refine.entry_id 7KUB _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 4 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 processing NMRPipe ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 2 'chemical shift assignment' NMRViewJ ? 'Johnson, Bruce' 3 'structure calculation' CYANA ? 'Guntert, Mumenthaler and Wuthrich' 4 refinement 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 U OP3 O N N 111 U P P N N 112 U OP1 O N N 113 U OP2 O N N 114 U "O5'" O N N 115 U "C5'" C N N 116 U "C4'" C N R 117 U "O4'" O N N 118 U "C3'" C N S 119 U "O3'" O N N 120 U "C2'" C N R 121 U "O2'" O N N 122 U "C1'" C N R 123 U N1 N N N 124 U C2 C N N 125 U O2 O N N 126 U N3 N N N 127 U C4 C N N 128 U O4 O N N 129 U C5 C N N 130 U C6 C N N 131 U HOP3 H N N 132 U HOP2 H N N 133 U "H5'" H N N 134 U "H5''" H N N 135 U "H4'" H N N 136 U "H3'" H N N 137 U "HO3'" H N N 138 U "H2'" H N N 139 U "HO2'" H N N 140 U "H1'" H N N 141 U H3 H N N 142 U H5 H N N 143 U H6 H N N 144 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7KUB 'double helix' 7KUB 'a-form double helix' 7KUB 'hairpin loop' 7KUB 'bulge loop' 7KUB 'mismatched base pair' 7KUB 'internal loop' 7KUB 'triple 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 C 1 1_555 A G 60 1_555 -0.622 0.056 0.006 4.375 -0.966 -0.316 1 A_C43:G102_A A 43 ? A 102 ? 19 1 1 A U 2 1_555 A A 59 1_555 -0.980 -0.047 -0.069 7.313 -5.318 -4.290 2 A_U44:A101_A A 44 ? A 101 ? 20 1 1 A G 3 1_555 A C 58 1_555 -0.104 0.080 0.123 0.378 -9.771 -1.028 3 A_G45:C100_A A 45 ? A 100 ? 19 1 1 A C 4 1_555 A G 57 1_555 0.338 0.028 0.128 -0.276 -9.836 -0.851 4 A_C46:G99_A A 46 ? A 99 ? 19 1 1 A U 5 1_555 A G 56 1_555 1.397 -0.319 0.251 -4.813 -10.366 -3.957 5 A_U47:G98_A A 47 ? A 98 ? 28 1 1 A C 6 1_555 A G 55 1_555 0.760 -0.321 0.631 -6.622 -12.553 -2.795 6 A_C48:G97_A A 48 ? A 97 ? 19 1 1 A U 7 1_555 A A 54 1_555 -0.662 0.036 0.353 -0.170 -8.099 -9.857 7 A_U49:A96_A A 49 ? A 96 ? 20 1 1 A C 9 1_555 A G 53 1_555 -0.725 -0.183 0.904 -1.463 3.944 1.639 8 A_C51:G95_A A 51 ? A 95 ? 19 1 1 A C 10 1_555 A G 52 1_555 -0.324 0.074 0.248 2.821 6.013 0.339 9 A_C52:G94_A A 52 ? A 94 ? 19 1 1 A U 11 1_555 A A 51 1_555 -0.081 -0.058 -0.448 5.088 7.755 -7.192 10 A_U53:A93_A A 53 ? A 93 ? 20 1 1 A U 12 1_555 A A 50 1_555 0.206 -0.208 0.179 5.071 -3.504 -1.353 11 A_U54:A92_A A 54 ? A 92 ? 20 1 1 A C 13 1_555 A G 49 1_555 -0.591 0.032 -0.294 -3.892 1.846 0.041 12 A_C55:G91_A A 55 ? A 91 ? 19 1 1 A C 15 1_555 A G 46 1_555 -0.631 -0.241 0.992 0.601 6.172 3.153 13 A_C57:G88_A A 57 ? A 88 ? 19 1 1 A C 16 1_555 A G 45 1_555 -0.382 0.013 0.429 4.842 -0.142 1.196 14 A_C58:G87_A A 58 ? A 87 ? 19 1 1 A A 17 1_555 A U 44 1_555 -0.307 0.004 0.023 2.160 -5.258 -6.188 15 A_A59:U86_A A 59 ? A 86 ? 20 1 1 A U 18 1_555 A A 43 1_555 -0.440 0.017 -0.042 3.037 -9.122 -6.910 16 A_U60:A85_A A 60 ? A 85 ? 20 1 1 A G 19 1_555 A C 42 1_555 0.595 -0.090 0.457 1.417 -13.731 -1.328 17 A_G61:C84_A A 61 ? A 84 ? 19 1 1 A C 20 1_555 A C 41 1_555 1.725 -1.140 0.267 -8.368 -13.874 -12.550 18 A_C62:C83_A A 62 ? A 83 ? ? ? 1 A C 21 1_555 A C 40 1_555 -2.297 -1.007 -0.044 1.178 -5.761 -23.248 19 A_C63:C82_A A 63 ? A 82 ? ? ? 1 A A 22 1_555 A A 39 1_555 -1.552 1.343 -0.013 -3.934 -7.929 -9.666 20 A_A64:A81_A A 64 ? A 81 ? ? 1 1 A G 24 1_555 A C 38 1_555 0.276 0.011 0.742 6.117 4.849 0.015 21 A_G66:C80_A A 66 ? A 80 ? 19 1 1 A U 25 1_555 A G 37 1_555 1.363 -0.353 0.406 -1.415 -1.605 -3.333 22 A_U67:G79_A A 67 ? A 79 ? 28 1 1 A G 26 1_555 A U 36 1_555 -1.368 -0.429 0.640 4.847 0.154 -1.563 23 A_G68:U78_A A 68 ? A 78 ? 28 1 1 A G 27 1_555 A C 35 1_555 0.040 0.092 0.036 -1.371 5.309 0.225 24 A_G69:C77_A A 69 ? A 77 ? 19 1 1 A U 28 1_555 A G 34 1_555 1.770 -0.278 -0.238 -3.594 15.801 -4.345 25 A_U70:G76_A A 70 ? A 76 ? 28 1 1 A C 29 1_555 A G 33 1_555 0.872 -0.343 -0.432 17.558 17.176 -1.906 26 A_C71:G75_A A 71 ? A 75 ? 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 C 1 1_555 A G 60 1_555 A U 2 1_555 A A 59 1_555 -0.348 -1.792 3.074 -1.257 13.469 28.364 -5.404 0.449 2.046 25.719 2.400 31.365 1 AA_C43U44:A101G102_AA A 43 ? A 102 ? A 44 ? A 101 ? 1 A U 2 1_555 A A 59 1_555 A G 3 1_555 A C 58 1_555 0.087 -1.402 3.640 -0.793 8.502 34.570 -3.612 -0.265 3.214 14.042 1.310 35.577 2 AA_U44G45:C100A101_AA A 44 ? A 101 ? A 45 ? A 100 ? 1 A G 3 1_555 A C 58 1_555 A C 4 1_555 A G 57 1_555 -0.014 -1.549 3.211 0.294 10.989 32.060 -4.268 0.067 2.556 19.205 -0.514 33.846 3 AA_G45C46:G99C100_AA A 45 ? A 100 ? A 46 ? A 99 ? 1 A C 4 1_555 A G 57 1_555 A U 5 1_555 A G 56 1_555 -0.124 -1.313 3.562 0.744 7.626 35.481 -3.228 0.308 3.217 12.337 -1.204 36.273 4 AA_C46U47:G98G99_AA A 46 ? A 99 ? A 47 ? A 98 ? 1 A U 5 1_555 A G 56 1_555 A C 6 1_555 A G 55 1_555 0.097 -1.589 3.342 0.526 7.799 30.225 -4.383 -0.085 2.854 14.651 -0.988 31.197 5 AA_U47C48:G97G98_AA A 47 ? A 98 ? A 48 ? A 97 ? 1 A C 6 1_555 A G 55 1_555 A U 7 1_555 A A 54 1_555 -0.323 -1.603 2.971 2.001 7.638 26.727 -4.863 1.073 2.400 16.081 -4.214 27.849 6 AA_C48U49:A96G97_AA A 48 ? A 97 ? A 49 ? A 96 ? 1 A U 7 1_555 A A 54 1_555 A C 9 1_555 A G 53 1_555 -1.062 -2.175 5.200 11.692 15.332 45.448 -4.297 2.559 3.947 18.875 -14.394 49.169 7 AA_U49C51:G95A96_AA A 49 ? A 96 ? A 51 ? A 95 ? 1 A C 9 1_555 A G 53 1_555 A C 10 1_555 A G 52 1_555 -0.091 -1.582 3.376 1.477 11.242 28.860 -5.017 0.440 2.586 21.537 -2.829 30.963 8 AA_C51C52:G94G95_AA A 51 ? A 95 ? A 52 ? A 94 ? 1 A C 10 1_555 A G 52 1_555 A U 11 1_555 A A 51 1_555 -0.478 -1.659 3.492 1.810 13.923 28.389 -5.503 1.197 2.402 26.441 -3.437 31.607 9 AA_C52U53:A93G94_AA A 52 ? A 94 ? A 53 ? A 93 ? 1 A U 11 1_555 A A 51 1_555 A U 12 1_555 A A 50 1_555 0.347 -1.670 3.418 -2.049 14.412 30.149 -5.133 -0.920 2.368 25.894 3.681 33.406 10 AA_U53U54:A92A93_AA A 53 ? A 93 ? A 54 ? A 92 ? 1 A U 12 1_555 A A 50 1_555 A C 13 1_555 A G 49 1_555 0.120 -1.962 3.902 0.367 10.166 27.831 -6.189 -0.150 3.015 20.297 -0.733 29.597 11 AA_U54C55:G91A92_AA A 54 ? A 92 ? A 55 ? A 91 ? 1 A C 13 1_555 A G 49 1_555 A C 15 1_555 A G 46 1_555 -0.115 -1.712 5.602 5.974 16.881 56.921 -3.135 0.614 4.929 17.247 -6.103 59.445 12 AA_C55C57:G88G91_AA A 55 ? A 91 ? A 57 ? A 88 ? 1 A C 15 1_555 A G 46 1_555 A C 16 1_555 A G 45 1_555 -0.162 -1.622 3.364 1.419 13.280 28.384 -5.319 0.548 2.375 25.383 -2.712 31.310 13 AA_C57C58:G87G88_AA A 57 ? A 88 ? A 58 ? A 87 ? 1 A C 16 1_555 A G 45 1_555 A A 17 1_555 A U 44 1_555 -0.407 -1.577 3.542 1.332 10.655 30.439 -4.742 0.971 2.824 19.545 -2.443 32.236 14 AA_C58A59:U86G87_AA A 58 ? A 87 ? A 59 ? A 86 ? 1 A A 17 1_555 A U 44 1_555 A U 18 1_555 A A 43 1_555 -0.086 -1.660 3.319 -0.095 8.455 29.359 -4.743 0.145 2.745 16.261 0.183 30.527 15 AA_A59U60:A85U86_AA A 59 ? A 86 ? A 60 ? A 85 ? 1 A U 18 1_555 A A 43 1_555 A G 19 1_555 A C 42 1_555 0.296 -1.284 3.400 -1.635 4.590 35.546 -2.751 -0.718 3.199 7.476 2.663 35.868 16 AA_U60G61:C84A85_AA A 60 ? A 85 ? A 61 ? A 84 ? 1 A G 19 1_555 A C 42 1_555 A C 20 1_555 A C 41 1_555 -0.746 -1.303 3.799 1.186 6.631 38.725 -2.827 1.269 3.514 9.908 -1.773 39.285 17 AA_G61C62:C83C84_AA A 61 ? A 84 ? A 62 ? A 83 ? 1 A C 20 1_555 A C 41 1_555 A C 21 1_555 A C 40 1_555 -0.740 -1.774 2.598 0.271 14.249 19.820 -6.984 1.805 1.083 35.988 -0.684 24.370 18 AA_C62C63:C82C83_AA A 62 ? A 83 ? A 63 ? A 82 ? 1 A C 21 1_555 A C 40 1_555 A A 22 1_555 A A 39 1_555 0.915 -1.537 3.706 0.239 9.051 35.845 -3.744 -1.409 3.242 14.425 -0.381 36.934 19 AA_C63A64:A81C82_AA A 63 ? A 82 ? A 64 ? A 81 ? 1 A A 22 1_555 A A 39 1_555 A G 24 1_555 A C 38 1_555 -1.028 -2.037 4.709 11.067 12.215 48.099 -3.535 2.248 3.810 14.500 -13.137 50.685 20 AA_A64G66:C80A81_AA A 64 ? A 81 ? A 66 ? A 80 ? 1 A G 24 1_555 A C 38 1_555 A U 25 1_555 A G 37 1_555 -0.163 -1.552 3.906 3.000 13.700 33.272 -4.660 0.735 3.029 22.712 -4.974 36.029 21 AA_G66U67:G79C80_AA A 66 ? A 80 ? A 67 ? A 79 ? 1 A U 25 1_555 A G 37 1_555 A G 26 1_555 A U 36 1_555 0.067 -1.985 2.902 -1.664 13.468 21.102 -7.431 -0.506 1.391 32.766 4.048 25.047 22 AA_U67G68:U78G79_AA A 67 ? A 79 ? A 68 ? A 78 ? 1 A G 26 1_555 A U 36 1_555 A G 27 1_555 A C 35 1_555 0.056 -1.522 3.883 1.164 10.312 35.128 -4.022 0.092 3.320 16.642 -1.878 36.583 23 AA_G68G69:C77U78_AA A 68 ? A 78 ? A 69 ? A 77 ? 1 A G 27 1_555 A C 35 1_555 A U 28 1_555 A G 34 1_555 -0.415 -1.480 3.941 1.566 11.003 34.253 -4.180 0.926 3.303 18.101 -2.577 35.960 24 AA_G69U70:G76C77_AA A 69 ? A 77 ? A 70 ? A 76 ? 1 A U 28 1_555 A G 34 1_555 A C 29 1_555 A G 33 1_555 -0.140 -1.917 2.760 1.579 12.810 19.753 -7.587 0.699 1.278 33.152 -4.086 23.561 25 AA_U70C71:G75G76_AA A 70 ? A 76 ? A 71 ? A 75 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Howard Hughes Medical Institute (HHMI)' 'United States' 55108516 1 'National Science Foundation (NSF, United States)' 'United States' 1144152 2 # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model Ascend800 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.details ? # _atom_sites.entry_id 7KUB _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.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_