data_8YNP # _entry.id 8YNP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.399 _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 8YNP pdb_00008ynp 10.2210/pdb8ynp/pdb WWPDB D_1300046012 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2025-01-22 # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8YNP _pdbx_database_status.recvd_initial_deposition_date 2024-03-11 _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 ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name PDB _pdbx_database_related.details . _pdbx_database_related.db_id 8YNO _pdbx_database_related.content_type unspecified # _pdbx_contact_author.id 2 _pdbx_contact_author.email j.kondo@sophia.ac.jp _pdbx_contact_author.name_first Jiro _pdbx_contact_author.name_last Kondo _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-5682-3685 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kondo, J.' 1 ? 'Abe, H.' 2 ? # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 52 _citation.language ? _citation.page_first 10754 _citation.page_last 10774 _citation.title ;Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs. ; _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkae741 _citation.pdbx_database_id_PubMed 39231537 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nomura, K.' 1 ? primary 'An, S.' 2 ? primary 'Kobayashi, Y.' 3 ? primary 'Kondo, J.' 4 0000-0002-5682-3685 primary 'Shi, T.' 5 ? primary 'Murase, H.' 6 ? primary 'Nakamoto, K.' 7 ? primary 'Kimura, Y.' 8 ? primary 'Abe, N.' 9 ? primary 'Ui-Tei, K.' 10 0000-0001-8695-9025 primary 'Abe, H.' 11 0000-0003-0048-3789 # 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 ;RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHX)P*CP*C)-3') ; 3947.284 2 ? ? ? ? 2 water nat water 18.015 170 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GGAC(5BU)CGAG(HHX)CC' _entity_poly.pdbx_seq_one_letter_code_can GGACUCGAGXCC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 A n 1 4 C n 1 5 5BU n 1 6 C n 1 7 G n 1 8 A n 1 9 G n 1 10 HHX n 1 11 C n 1 12 C 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 12 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 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 HHX 'RNA linking' . ;[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-[methanoyl(methyl)amino]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate ; ? 'C11 H16 N3 O9 P' 365.233 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 5BU 5 5 5 5BU 5BU A . n A 1 6 C 6 6 6 C C A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 G 9 9 9 G G A . n A 1 10 HHX 10 10 10 HHX HHX A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 G 2 2 2 G G B . n B 1 3 A 3 3 3 A A B . n B 1 4 C 4 4 4 C C B . n B 1 5 5BU 5 5 5 5BU 5BU B . n B 1 6 C 6 6 6 C C B . n B 1 7 G 7 7 7 G G B . n B 1 8 A 8 8 8 A A B . n B 1 9 G 9 9 9 G G B . n B 1 10 HHX 10 10 10 HHX HHX B . n B 1 11 C 11 11 11 C C B . n B 1 12 C 12 12 12 C C B . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id HHX _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id HHX _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 2 HOH 1 101 101 HOH HOH A . C 2 HOH 2 102 102 HOH HOH A . C 2 HOH 3 103 103 HOH HOH A . C 2 HOH 4 104 104 HOH HOH A . C 2 HOH 5 105 105 HOH HOH A . C 2 HOH 6 106 106 HOH HOH A . C 2 HOH 7 107 107 HOH HOH A . C 2 HOH 8 108 108 HOH HOH A . C 2 HOH 9 109 109 HOH HOH A . C 2 HOH 10 110 110 HOH HOH A . C 2 HOH 11 111 111 HOH HOH A . C 2 HOH 12 112 112 HOH HOH A . C 2 HOH 13 113 113 HOH HOH A . C 2 HOH 14 114 114 HOH HOH A . C 2 HOH 15 115 115 HOH HOH A . C 2 HOH 16 116 116 HOH HOH A . C 2 HOH 17 117 117 HOH HOH A . C 2 HOH 18 118 118 HOH HOH A . C 2 HOH 19 119 119 HOH HOH A . C 2 HOH 20 120 120 HOH HOH A . C 2 HOH 21 121 121 HOH HOH A . C 2 HOH 22 122 122 HOH HOH A . C 2 HOH 23 123 123 HOH HOH A . C 2 HOH 24 124 124 HOH HOH A . C 2 HOH 25 125 125 HOH HOH A . C 2 HOH 26 126 126 HOH HOH A . C 2 HOH 27 127 127 HOH HOH A . C 2 HOH 28 128 128 HOH HOH A . C 2 HOH 29 129 129 HOH HOH A . C 2 HOH 30 130 130 HOH HOH A . C 2 HOH 31 131 131 HOH HOH A . C 2 HOH 32 132 132 HOH HOH A . C 2 HOH 33 133 133 HOH HOH A . C 2 HOH 34 134 134 HOH HOH A . C 2 HOH 35 135 136 HOH HOH A . C 2 HOH 36 136 135 HOH HOH A . C 2 HOH 37 137 137 HOH HOH A . C 2 HOH 38 138 138 HOH HOH A . C 2 HOH 39 139 139 HOH HOH A . C 2 HOH 40 140 140 HOH HOH A . C 2 HOH 41 141 141 HOH HOH A . C 2 HOH 42 142 142 HOH HOH A . C 2 HOH 43 143 143 HOH HOH A . C 2 HOH 44 144 144 HOH HOH A . C 2 HOH 45 145 145 HOH HOH A . C 2 HOH 46 146 146 HOH HOH A . C 2 HOH 47 147 147 HOH HOH A . C 2 HOH 48 148 148 HOH HOH A . C 2 HOH 49 149 149 HOH HOH A . C 2 HOH 50 150 150 HOH HOH A . C 2 HOH 51 151 151 HOH HOH A . C 2 HOH 52 152 152 HOH HOH A . C 2 HOH 53 153 153 HOH HOH A . C 2 HOH 54 154 154 HOH HOH A . C 2 HOH 55 155 155 HOH HOH A . C 2 HOH 56 156 156 HOH HOH A . C 2 HOH 57 157 157 HOH HOH A . C 2 HOH 58 158 158 HOH HOH A . C 2 HOH 59 159 159 HOH HOH A . C 2 HOH 60 160 160 HOH HOH A . C 2 HOH 61 161 161 HOH HOH A . C 2 HOH 62 162 162 HOH HOH A . C 2 HOH 63 163 163 HOH HOH A . C 2 HOH 64 164 164 HOH HOH A . C 2 HOH 65 165 165 HOH HOH A . C 2 HOH 66 166 166 HOH HOH A . C 2 HOH 67 167 167 HOH HOH A . C 2 HOH 68 168 168 HOH HOH A . C 2 HOH 69 169 169 HOH HOH A . C 2 HOH 70 170 170 HOH HOH A . C 2 HOH 71 171 171 HOH HOH A . C 2 HOH 72 172 172 HOH HOH A . C 2 HOH 73 173 173 HOH HOH A . C 2 HOH 74 174 174 HOH HOH A . C 2 HOH 75 175 175 HOH HOH A . C 2 HOH 76 176 176 HOH HOH A . C 2 HOH 77 177 177 HOH HOH A . C 2 HOH 78 178 178 HOH HOH A . C 2 HOH 79 179 179 HOH HOH A . C 2 HOH 80 180 180 HOH HOH A . C 2 HOH 81 181 181 HOH HOH A . C 2 HOH 82 182 182 HOH HOH A . C 2 HOH 83 183 183 HOH HOH A . D 2 HOH 1 101 101 HOH HOH B . D 2 HOH 2 102 102 HOH HOH B . D 2 HOH 3 103 103 HOH HOH B . D 2 HOH 4 104 104 HOH HOH B . D 2 HOH 5 105 105 HOH HOH B . D 2 HOH 6 106 106 HOH HOH B . D 2 HOH 7 107 107 HOH HOH B . D 2 HOH 8 108 108 HOH HOH B . D 2 HOH 9 109 109 HOH HOH B . D 2 HOH 10 110 110 HOH HOH B . D 2 HOH 11 111 111 HOH HOH B . D 2 HOH 12 112 112 HOH HOH B . D 2 HOH 13 113 113 HOH HOH B . D 2 HOH 14 114 114 HOH HOH B . D 2 HOH 15 115 115 HOH HOH B . D 2 HOH 16 116 116 HOH HOH B . D 2 HOH 17 117 117 HOH HOH B . D 2 HOH 18 118 118 HOH HOH B . D 2 HOH 19 119 119 HOH HOH B . D 2 HOH 20 120 120 HOH HOH B . D 2 HOH 21 121 121 HOH HOH B . D 2 HOH 22 122 122 HOH HOH B . D 2 HOH 23 123 123 HOH HOH B . D 2 HOH 24 124 124 HOH HOH B . D 2 HOH 25 125 125 HOH HOH B . D 2 HOH 26 126 126 HOH HOH B . D 2 HOH 27 127 127 HOH HOH B . D 2 HOH 28 128 128 HOH HOH B . D 2 HOH 29 129 129 HOH HOH B . D 2 HOH 30 130 130 HOH HOH B . D 2 HOH 31 131 131 HOH HOH B . D 2 HOH 32 132 132 HOH HOH B . D 2 HOH 33 133 133 HOH HOH B . D 2 HOH 34 134 134 HOH HOH B . D 2 HOH 35 135 135 HOH HOH B . D 2 HOH 36 136 136 HOH HOH B . D 2 HOH 37 137 137 HOH HOH B . D 2 HOH 38 138 138 HOH HOH B . D 2 HOH 39 139 139 HOH HOH B . D 2 HOH 40 140 140 HOH HOH B . D 2 HOH 41 141 141 HOH HOH B . D 2 HOH 42 142 142 HOH HOH B . D 2 HOH 43 143 143 HOH HOH B . D 2 HOH 44 144 144 HOH HOH B . D 2 HOH 45 145 145 HOH HOH B . D 2 HOH 46 146 146 HOH HOH B . D 2 HOH 47 147 147 HOH HOH B . D 2 HOH 48 148 148 HOH HOH B . D 2 HOH 49 149 149 HOH HOH B . D 2 HOH 50 150 150 HOH HOH B . D 2 HOH 51 151 151 HOH HOH B . D 2 HOH 52 152 152 HOH HOH B . D 2 HOH 53 153 153 HOH HOH B . D 2 HOH 54 154 154 HOH HOH B . D 2 HOH 55 155 155 HOH HOH B . D 2 HOH 56 156 156 HOH HOH B . D 2 HOH 57 157 157 HOH HOH B . D 2 HOH 58 158 158 HOH HOH B . D 2 HOH 59 159 159 HOH HOH B . D 2 HOH 60 160 160 HOH HOH B . D 2 HOH 61 161 161 HOH HOH B . D 2 HOH 62 162 162 HOH HOH B . D 2 HOH 63 163 163 HOH HOH B . D 2 HOH 64 164 164 HOH HOH B . D 2 HOH 65 165 165 HOH HOH B . D 2 HOH 66 166 166 HOH HOH B . D 2 HOH 67 167 167 HOH HOH B . D 2 HOH 68 168 168 HOH HOH B . D 2 HOH 69 169 169 HOH HOH B . D 2 HOH 70 170 170 HOH HOH B . D 2 HOH 71 171 171 HOH HOH B . D 2 HOH 72 172 172 HOH HOH B . D 2 HOH 73 173 173 HOH HOH B . D 2 HOH 74 174 174 HOH HOH B . D 2 HOH 75 175 175 HOH HOH B . D 2 HOH 76 176 176 HOH HOH B . D 2 HOH 77 177 177 HOH HOH B . D 2 HOH 78 178 178 HOH HOH B . D 2 HOH 79 179 179 HOH HOH B . D 2 HOH 80 180 180 HOH HOH B . D 2 HOH 81 181 181 HOH HOH B . D 2 HOH 82 182 182 HOH HOH B . D 2 HOH 83 183 183 HOH HOH B . D 2 HOH 84 184 184 HOH HOH B . D 2 HOH 85 185 185 HOH HOH B . D 2 HOH 86 186 186 HOH HOH B . D 2 HOH 87 187 187 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1_3660 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.27 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 110.030 _cell.angle_alpha_esd ? _cell.angle_beta 114.810 _cell.angle_beta_esd ? _cell.angle_gamma 95.760 _cell.angle_gamma_esd ? _cell.entry_id 8YNP _cell.details ? _cell.formula_units_Z ? _cell.length_a 25.604 _cell.length_a_esd ? _cell.length_b 27.932 _cell.length_b_esd ? _cell.length_c 28.668 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 2 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8YNP _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _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 8YNP _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.25 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 45.21 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'MPD, sodium cacodylate, spermine tetrahydrochloride' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2020-11-29 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.91962 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.91962 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 18.341 _reflns.entry_id 8YNP _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.400 _reflns.d_resolution_low 25.150 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 12164 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 93.900 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.576 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 12.580 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.963 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.084 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 43501 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.993 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.071 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 1.400 1.430 ? 7.070 ? 3121 942 ? 841 ? ? ? ? ? ? ? ? ? ? ? 3.711 ? ? ? 0.270 ? ? 1 1 0.950 ? ? 89.300 ? 0.231 ? ? ? ? ? ? ? ? ? 1.430 1.470 ? 7.620 ? 3269 948 ? 884 ? ? ? ? ? ? ? ? ? ? ? 3.698 ? ? ? 0.247 ? ? 2 1 0.965 ? ? 93.200 ? 0.211 ? ? ? ? ? ? ? ? ? 1.470 1.520 ? 8.210 ? 3038 897 ? 831 ? ? ? ? ? ? ? ? ? ? ? 3.656 ? ? ? 0.219 ? ? 3 1 0.959 ? ? 92.600 ? 0.187 ? ? ? ? ? ? ? ? ? 1.520 1.560 ? 8.760 ? 2966 871 ? 823 ? ? ? ? ? ? ? ? ? ? ? 3.604 ? ? ? 0.196 ? ? 4 1 0.965 ? ? 94.500 ? 0.166 ? ? ? ? ? ? ? ? ? 1.560 1.610 ? 9.900 ? 2792 863 ? 805 ? ? ? ? ? ? ? ? ? ? ? 3.468 ? ? ? 0.155 ? ? 5 1 0.984 ? ? 93.300 ? 0.131 ? ? ? ? ? ? ? ? ? 1.610 1.670 ? 10.480 ? 2462 809 ? 749 ? ? ? ? ? ? ? ? ? ? ? 3.287 ? ? ? 0.126 ? ? 6 1 0.986 ? ? 92.600 ? 0.104 ? ? ? ? ? ? ? ? ? 1.670 1.730 ? 12.190 ? 2790 815 ? 761 ? ? ? ? ? ? ? ? ? ? ? 3.666 ? ? ? 0.112 ? ? 7 1 0.990 ? ? 93.400 ? 0.095 ? ? ? ? ? ? ? ? ? 1.730 1.800 ? 13.410 ? 2752 780 ? 737 ? ? ? ? ? ? ? ? ? ? ? 3.734 ? ? ? 0.104 ? ? 8 1 0.987 ? ? 94.500 ? 0.089 ? ? ? ? ? ? ? ? ? 1.800 1.880 ? 13.800 ? 2512 713 ? 676 ? ? ? ? ? ? ? ? ? ? ? 3.716 ? ? ? 0.100 ? ? 9 1 0.988 ? ? 94.800 ? 0.086 ? ? ? ? ? ? ? ? ? 1.880 1.980 ? 14.440 ? 2495 716 ? 682 ? ? ? ? ? ? ? ? ? ? ? 3.658 ? ? ? 0.092 ? ? 10 1 0.989 ? ? 95.300 ? 0.079 ? ? ? ? ? ? ? ? ? 1.980 2.080 ? 14.930 ? 2254 666 ? 628 ? ? ? ? ? ? ? ? ? ? ? 3.589 ? ? ? 0.084 ? ? 11 1 0.992 ? ? 94.300 ? 0.071 ? ? ? ? ? ? ? ? ? 2.080 2.210 ? 15.330 ? 2130 636 ? 608 ? ? ? ? ? ? ? ? ? ? ? 3.503 ? ? ? 0.082 ? ? 12 1 0.992 ? ? 95.600 ? 0.069 ? ? ? ? ? ? ? ? ? 2.210 2.360 ? 15.080 ? 1814 608 ? 568 ? ? ? ? ? ? ? ? ? ? ? 3.194 ? ? ? 0.079 ? ? 13 1 0.988 ? ? 93.400 ? 0.065 ? ? ? ? ? ? ? ? ? 2.360 2.550 ? 16.940 ? 1947 554 ? 533 ? ? ? ? ? ? ? ? ? ? ? 3.653 ? ? ? 0.074 ? ? 14 1 0.993 ? ? 96.200 ? 0.063 ? ? ? ? ? ? ? ? ? 2.550 2.790 ? 17.370 ? 1813 512 ? 487 ? ? ? ? ? ? ? ? ? ? ? 3.723 ? ? ? 0.076 ? ? 15 1 0.990 ? ? 95.100 ? 0.065 ? ? ? ? ? ? ? ? ? 2.790 3.120 ? 17.480 ? 1584 459 ? 441 ? ? ? ? ? ? ? ? ? ? ? 3.592 ? ? ? 0.084 ? ? 16 1 0.991 ? ? 96.100 ? 0.071 ? ? ? ? ? ? ? ? ? 3.120 3.610 ? 17.990 ? 1389 414 ? 395 ? ? ? ? ? ? ? ? ? ? ? 3.516 ? ? ? 0.085 ? ? 17 1 0.989 ? ? 95.400 ? 0.072 ? ? ? ? ? ? ? ? ? 3.610 4.420 ? 17.100 ? 987 331 ? 312 ? ? ? ? ? ? ? ? ? ? ? 3.163 ? ? ? 0.067 ? ? 18 1 0.993 ? ? 94.300 ? 0.055 ? ? ? ? ? ? ? ? ? 4.420 6.250 ? 18.020 ? 891 266 ? 255 ? ? ? ? ? ? ? ? ? ? ? 3.494 ? ? ? 0.058 ? ? 19 1 0.997 ? ? 95.900 ? 0.049 ? ? ? ? ? ? ? ? ? 6.250 25.150 ? 17.530 ? 495 153 ? 148 ? ? ? ? ? ? ? ? ? ? ? 3.345 ? ? ? 0.063 ? ? 20 1 0.994 ? ? 96.700 ? 0.053 ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 38.830 _refine.B_iso_mean 13.8460 _refine.B_iso_min 6.090 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8YNP _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.4000 _refine.ls_d_res_low 25.1500 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 12149 _refine.ls_number_reflns_R_free 1216 _refine.ls_number_reflns_R_work 10933 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 94.4500 _refine.ls_percent_reflns_R_free 10.0100 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1537 _refine.ls_R_factor_R_free 0.1725 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1515 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.080 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 18.2000 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.0900 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 1.4000 _refine_hist.d_res_low 25.1500 _refine_hist.number_atoms_solvent 170 _refine_hist.number_atoms_total 684 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total 24 _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent 23.29 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 514 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.4000 1.4500 1261 . 126 1135 90.0000 . . . 0.0000 0.1757 . . . . . . . 9 . . . 0.2106 'X-RAY DIFFRACTION' 1.4500 1.5200 1370 . 137 1233 94.0000 . . . 0.0000 0.1667 . . . . . . . 9 . . . 0.1974 'X-RAY DIFFRACTION' 1.5200 1.6000 1341 . 134 1207 94.0000 . . . 0.0000 0.1569 . . . . . . . 9 . . . 0.2081 'X-RAY DIFFRACTION' 1.6000 1.7000 1326 . 132 1194 93.0000 . . . 0.0000 0.1427 . . . . . . . 9 . . . 0.1805 'X-RAY DIFFRACTION' 1.7000 1.8300 1358 . 136 1222 95.0000 . . . 0.0000 0.1453 . . . . . . . 9 . . . 0.1533 'X-RAY DIFFRACTION' 1.8300 2.0100 1367 . 137 1230 96.0000 . . . 0.0000 0.1508 . . . . . . . 9 . . . 0.1698 'X-RAY DIFFRACTION' 2.0100 2.3100 1364 . 137 1227 95.0000 . . . 0.0000 0.1600 . . . . . . . 9 . . . 0.1889 'X-RAY DIFFRACTION' 2.3100 2.9000 1382 . 138 1244 97.0000 . . . 0.0000 0.1769 . . . . . . . 9 . . . 0.2017 'X-RAY DIFFRACTION' 2.9100 25.1500 1380 . 139 1241 96.0000 . . . 0.0000 0.1325 . . . . . . . 9 . . . 0.1404 # _struct.entry_id 8YNP _struct.title 'RNA duplex containing Methylformamide' _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 8YNP _struct_keywords.text 'Methylformamide, RNA' _struct_keywords.pdbx_keywords RNA # 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 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8YNP _struct_ref.pdbx_db_accession 8YNP _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 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 8YNP A 1 ? 12 ? 8YNP 1 ? 12 ? 1 12 2 1 8YNP B 1 ? 12 ? 8YNP 1 ? 12 ? 1 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 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)' 2310 ? 1 MORE 4 ? 1 'SSA (A^2)' 4350 ? # _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 none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 covale1 covale both ? A C 4 "O3'" ? ? ? 1_555 A 5BU 5 P ? ? A C 4 A 5BU 5 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale2 covale both ? A 5BU 5 "O3'" ? ? ? 1_555 A C 6 P ? ? A 5BU 5 A C 6 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale both ? A G 9 "O3'" ? ? ? 1_555 A HHX 10 P ? ? A G 9 A HHX 10 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale4 covale both ? A HHX 10 "O3'" ? ? ? 1_555 A C 11 P ? ? A HHX 10 A C 11 1_555 ? ? ? ? ? ? ? 1.589 ? ? covale5 covale both ? B C 4 "O3'" ? ? ? 1_555 B 5BU 5 P ? ? B C 4 B 5BU 5 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale6 covale both ? B 5BU 5 "O3'" ? ? ? 1_555 B C 6 P ? ? B 5BU 5 B C 6 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale7 covale both ? B G 9 "O3'" ? ? ? 1_555 B HHX 10 P ? ? B G 9 B HHX 10 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale8 covale both ? B HHX 10 "O3'" ? ? ? 1_555 B C 11 P ? ? B HHX 10 B C 11 1_555 ? ? ? ? ? ? ? 1.596 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 4 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 4 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 4 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 5BU 5 N3 ? ? ? 1_555 B A 8 N1 ? ? A 5BU 5 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A 5BU 5 O4 ? ? ? 1_555 B A 8 N6 ? ? A 5BU 5 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 7 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 7 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 7 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N1 ? ? ? 1_555 B 5BU 5 N3 ? ? A A 8 B 5BU 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 8 N6 ? ? ? 1_555 B 5BU 5 O4 ? ? A A 8 B 5BU 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 9 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 9 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 9 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_entry_details.entry_id 8YNP _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_ _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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HHX "C1'" C N R 145 HHX C2 C N N 146 HHX "C2'" C N R 147 HHX "C3'" C N S 148 HHX C4 C N N 149 HHX "C4'" C N R 150 HHX C5 C N N 151 HHX "C5'" C N N 152 HHX C6 C N N 153 HHX "C6'" C N N 154 HHX "C7'" C N N 155 HHX N1 N N N 156 HHX "N2'" N N N 157 HHX N3 N N N 158 HHX O2 O N N 159 HHX "O3'" O N N 160 HHX O4 O N N 161 HHX "O4'" O N N 162 HHX "O5'" O N N 163 HHX "O6'" O N N 164 HHX OP1 O N N 165 HHX OP2 O N N 166 HHX P P N N 167 HHX H1 H N N 168 HHX H2 H N N 169 HHX H3 H N N 170 HHX H4 H N N 171 HHX H5 H N N 172 HHX H6 H N N 173 HHX H7 H N N 174 HHX H8 H N N 175 HHX H9 H N N 176 HHX H10 H N N 177 HHX H11 H N N 178 HHX H12 H N N 179 HHX H13 H N N 180 HHX "HO3'" H N N 181 HHX HOP2 H N N 182 HHX OP3 O N N 183 HHX HOP3 H N N 184 HOH O O N N 185 HOH H1 H N N 186 HOH H2 H N N 187 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HHX "O3'" "C3'" sing N N 151 HHX "O6'" "C7'" doub N N 152 HHX "C7'" "N2'" sing N N 153 HHX "C3'" "C2'" sing N N 154 HHX "C3'" "C4'" sing N N 155 HHX "N2'" "C6'" sing N N 156 HHX "N2'" "C2'" sing N N 157 HHX "C2'" "C1'" sing N N 158 HHX "C4'" "C5'" sing N N 159 HHX "C4'" "O4'" sing N N 160 HHX "C5'" "O5'" sing N N 161 HHX OP1 P doub N N 162 HHX "O5'" P sing N N 163 HHX "C1'" "O4'" sing N N 164 HHX "C1'" N1 sing N N 165 HHX P OP2 sing N N 166 HHX O2 C2 doub N N 167 HHX N1 C2 sing N N 168 HHX N1 C6 sing N N 169 HHX C2 N3 sing N N 170 HHX C6 C5 doub N N 171 HHX N3 C4 sing N N 172 HHX C5 C4 sing N N 173 HHX C4 O4 doub N N 174 HHX "C1'" H1 sing N N 175 HHX "C2'" H2 sing N N 176 HHX "C3'" H3 sing N N 177 HHX "C4'" H4 sing N N 178 HHX C5 H5 sing N N 179 HHX "C5'" H6 sing N N 180 HHX "C5'" H7 sing N N 181 HHX C6 H8 sing N N 182 HHX "C6'" H9 sing N N 183 HHX "C6'" H10 sing N N 184 HHX "C6'" H11 sing N N 185 HHX "C7'" H12 sing N N 186 HHX N3 H13 sing N N 187 HHX "O3'" "HO3'" sing N N 188 HHX OP2 HOP2 sing N N 189 HHX P OP3 sing N N 190 HHX OP3 HOP3 sing N N 191 HOH O H1 sing N N 192 HOH O H2 sing N N 193 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8YNP 'double helix' 8YNP 'a-form 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 G 1 1_555 B C 12 1_555 -0.223 -0.147 0.019 2.212 -6.952 -1.430 1 A_G1:C12_B A 1 ? B 12 ? 19 1 1 A G 2 1_555 B C 11 1_555 -0.170 -0.177 -0.014 -7.274 -16.603 2.188 2 A_G2:C11_B A 2 ? B 11 ? 19 1 1 A C 4 1_555 B G 9 1_555 0.232 -0.153 0.121 1.889 -8.498 -0.891 3 A_C4:G9_B A 4 ? B 9 ? 19 1 1 A 5BU 5 1_555 B A 8 1_555 -0.082 -0.190 -0.166 9.619 -8.499 0.351 4 A_5BU5:A8_B A 5 ? B 8 ? 20 1 1 A C 6 1_555 B G 7 1_555 0.148 -0.106 -0.087 8.877 -15.672 1.173 5 A_C6:G7_B A 6 ? B 7 ? 19 1 1 A G 7 1_555 B C 6 1_555 -0.191 -0.116 -0.217 -6.466 -9.747 0.202 6 A_G7:C6_B A 7 ? B 6 ? 19 1 1 A A 8 1_555 B 5BU 5 1_555 0.093 -0.146 -0.153 -7.102 -11.668 -2.533 7 A_A8:5BU5_B A 8 ? B 5 ? 20 1 1 A G 9 1_555 B C 4 1_555 -0.150 -0.110 -0.009 -6.494 -9.480 1.709 8 A_G9:C4_B A 9 ? B 4 ? 19 1 1 A C 11 1_555 B G 2 1_555 0.340 -0.130 -0.082 6.784 -14.018 2.539 9 A_C11:G2_B A 11 ? B 2 ? 19 1 1 A C 12 1_555 B G 1 1_555 0.154 -0.110 0.031 1.517 -3.633 -2.046 10 A_C12:G1_B A 12 ? B 1 ? 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 G 1 1_555 B C 12 1_555 A G 2 1_555 B C 11 1_555 0.347 -2.177 3.397 0.285 8.709 34.024 -4.862 -0.534 2.775 14.589 -0.477 35.090 1 AA_G1G2:C11C12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A G 2 1_555 B C 11 1_555 A C 4 1_555 B G 9 1_555 -0.488 -2.759 6.135 -0.919 8.590 61.993 -3.369 0.394 5.752 8.297 0.888 62.532 2 AA_G2C4:G9C11_BB A 2 ? B 11 ? A 4 ? B 9 ? 1 A C 4 1_555 B G 9 1_555 A 5BU 5 1_555 B A 8 1_555 -1.201 -2.161 3.055 -0.997 6.012 23.354 -6.823 2.600 2.477 14.536 2.411 24.125 3 AA_C45BU5:A8G9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A 5BU 5 1_555 B A 8 1_555 A C 6 1_555 B G 7 1_555 0.563 -1.485 3.220 -0.109 8.939 34.827 -3.595 -0.927 2.766 14.638 0.179 35.922 4 AA_5BU5C6:G7A8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A C 6 1_555 B G 7 1_555 A G 7 1_555 B C 6 1_555 -0.493 -1.801 3.514 0.255 14.179 32.315 -5.014 0.852 2.523 24.080 -0.432 35.214 5 AA_C6G7:C6G7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A G 7 1_555 B C 6 1_555 A A 8 1_555 B 5BU 5 1_555 -0.114 -1.426 3.289 -0.008 5.280 31.914 -3.467 0.203 3.020 9.521 0.014 32.336 6 AA_G7A8:5BU5C6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A A 8 1_555 B 5BU 5 1_555 A G 9 1_555 B C 4 1_555 0.866 -2.123 3.244 1.386 5.305 29.421 -5.147 -1.407 2.863 10.332 -2.700 29.917 7 AA_A8G9:C45BU5_BB A 8 ? B 5 ? A 9 ? B 4 ? 1 A G 9 1_555 B C 4 1_555 A C 11 1_555 B G 2 1_555 0.132 -2.896 6.032 -0.603 12.968 60.033 -3.922 -0.179 5.363 12.800 0.595 61.293 8 AA_G9C11:G2C4_BB A 9 ? B 4 ? A 11 ? B 2 ? 1 A C 11 1_555 B G 2 1_555 A C 12 1_555 B G 1 1_555 -0.693 -2.035 3.325 -1.323 9.068 33.277 -4.758 0.976 2.718 15.472 2.257 34.481 9 AA_C11C12:G1G2_BB A 11 ? B 2 ? A 12 ? B 1 ? # _pdbx_audit_support.funding_organization 'Japan Science and Technology' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number JPMJCR18S1 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 8YNP _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] 0.039056 _atom_sites.fract_transf_matrix[1][2] 0.003940 _atom_sites.fract_transf_matrix[1][3] 0.021804 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.035983 _atom_sites.fract_transf_matrix[2][3] 0.016932 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.042469 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol BR C N O P # loop_ #