data_7Y8P # _entry.id 7Y8P # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 7Y8P pdb_00007y8p 10.2210/pdb7y8p/pdb WWPDB D_1300030495 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7Y8P _pdbx_database_status.recvd_initial_deposition_date 2022-06-24 _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 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kondo, J.' 1 0000-0002-5682-3685 'Minakawa, N.' 2 ? 'Ohta, M.' 3 ? 'Takahashi, H.' 4 ? 'Tarashima, N.' 5 ? # _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 Bioorg.Med.Chem. _citation.journal_id_ASTM BMECEP _citation.journal_id_CSD 1200 _citation.journal_id_ISSN 1464-3391 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 76 _citation.language ? _citation.page_first 117093 _citation.page_last 117093 _citation.title ;Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog. ; _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.bmc.2022.117093 _citation.pdbx_database_id_PubMed 36434923 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ota, M.' 1 ? primary 'Takahashi, H.' 2 ? primary 'Nogi, Y.' 3 ? primary 'Kagotani, Y.' 4 ? primary 'Saito-Tarashima, N.' 5 ? primary 'Kondo, J.' 6 ? primary 'Minakawa, N.' 7 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 113.470 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 7Y8P _cell.details ? _cell.formula_units_Z ? _cell.length_a 26.951 _cell.length_a_esd ? _cell.length_b 38.107 _cell.length_b_esd ? _cell.length_c 31.882 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _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 7Y8P _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? # 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*(IKS)P*(ILK)P*(IKS)P*GP*AP*GP*UP*CP*C)-3') ; 4016.217 2 ? ? ? ? 2 non-polymer nat 'COBALT HEXAMMINE(III)' 161.116 3 ? ? ? ? 3 water nat water 18.015 123 ? ? ? ? # _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 'GGA(IKS)(ILK)(IKS)GAGUCC' _entity_poly.pdbx_seq_one_letter_code_can GGAXXXGAGUCC _entity_poly.pdbx_strand_id A,B _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 G n 1 2 G n 1 3 A n 1 4 IKS n 1 5 ILK n 1 6 IKS n 1 7 G n 1 8 A n 1 9 G n 1 10 U 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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7Y8P _struct_ref.pdbx_db_accession 7Y8P _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 7Y8P A 1 ? 12 ? 7Y8P 1 ? 12 ? 1 12 2 1 7Y8P B 1 ? 12 ? 7Y8P 1 ? 12 ? 1 12 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 IKS 'RNA linking' . '[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)selenolan-2-yl]methyl dihydrogen phosphate' ? 'C9 H14 N3 O7 P Se' 386.157 ILK 'RNA linking' . '[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)selenolan-2-yl]methyl dihydrogen phosphate' ? 'C9 H13 N2 O8 P Se' 387.142 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _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 7Y8P _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 1.87 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 34.21 _exptl_crystal.description 'The entry contains friedel pairs in F_plus/minus columns' _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'MPD, sodium cacodylate, hexammine cobalt' _exptl_crystal_grow.pdbx_pH_range ? # _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 4M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-12-23 _diffrn_detector.pdbx_frequency ? # _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 1.1 _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-1A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-1A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 17.367 _reflns.entry_id 7Y8P _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.500 _reflns.d_resolution_low 29.250 _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 18427 _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 98.500 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.369 _reflns.pdbx_Rmerge_I_obs 0.080 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 11.180 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.105 _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 0.095 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 62087 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.994 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _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 ? _reflns.pdbx_CC_split_method ? # 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_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_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_Rsym_value _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.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 1.500 1.540 ? 4.240 ? 4352 1355 ? 1312 96.800 ? ? ? ? 0.281 ? ? ? ? ? ? ? ? 3.317 ? ? ? ? 0.336 ? ? 1 1 0.946 ? ? ? ? ? ? ? ? ? ? 1.540 1.580 ? 4.970 ? 4613 1368 ? 1353 98.900 ? ? ? ? 0.248 ? ? ? ? ? ? ? ? 3.409 ? ? ? ? 0.295 ? ? 2 1 0.966 ? ? ? ? ? ? ? ? ? ? 1.580 1.630 ? 6.140 ? 4316 1282 ? 1273 99.300 ? ? ? ? 0.186 ? ? ? ? ? ? ? ? 3.390 ? ? ? ? 0.221 ? ? 3 1 0.988 ? ? ? ? ? ? ? ? ? ? 1.630 1.680 ? 6.880 ? 4269 1299 ? 1287 99.100 ? ? ? ? 0.170 ? ? ? ? ? ? ? ? 3.317 ? ? ? ? 0.204 ? ? 4 1 0.982 ? ? ? ? ? ? ? ? ? ? 1.680 1.730 ? 7.910 ? 4078 1233 ? 1212 98.300 ? ? ? ? 0.152 ? ? ? ? ? ? ? ? 3.365 ? ? ? ? 0.181 ? ? 5 1 0.985 ? ? ? ? ? ? ? ? ? ? 1.730 1.790 ? 8.290 ? 3948 1218 ? 1211 99.400 ? ? ? ? 0.142 ? ? ? ? ? ? ? ? 3.260 ? ? ? ? 0.169 ? ? 6 1 0.980 ? ? ? ? ? ? ? ? ? ? 1.790 1.860 ? 9.420 ? 3634 1131 ? 1122 99.200 ? ? ? ? 0.126 ? ? ? ? ? ? ? ? 3.239 ? ? ? ? 0.151 ? ? 7 1 0.973 ? ? ? ? ? ? ? ? ? ? 1.860 1.940 ? 10.270 ? 3537 1124 ? 1103 98.100 ? ? ? ? 0.122 ? ? ? ? ? ? ? ? 3.207 ? ? ? ? 0.147 ? ? 8 1 0.977 ? ? ? ? ? ? ? ? ? ? 1.940 2.020 ? 10.950 ? 3253 1058 ? 1043 98.600 ? ? ? ? 0.106 ? ? ? ? ? ? ? ? 3.119 ? ? ? ? 0.129 ? ? 9 1 0.981 ? ? ? ? ? ? ? ? ? ? 2.020 2.120 ? 11.130 ? 2905 1031 ? 1000 97.000 ? ? ? ? 0.100 ? ? ? ? ? ? ? ? 2.905 ? ? ? ? 0.123 ? ? 10 1 0.979 ? ? ? ? ? ? ? ? ? ? 2.120 2.230 ? 13.070 ? 3245 967 ? 959 99.200 ? ? ? ? 0.118 ? ? ? ? ? ? ? ? 3.384 ? ? ? ? 0.140 ? ? 11 1 0.981 ? ? ? ? ? ? ? ? ? ? 2.230 2.370 ? 14.050 ? 2812 887 ? 881 99.300 ? ? ? ? 0.086 ? ? ? ? ? ? ? ? 3.192 ? ? ? ? 0.104 ? ? 12 1 0.988 ? ? ? ? ? ? ? ? ? ? 2.370 2.530 ? 15.740 ? 3131 858 ? 853 99.400 ? ? ? ? 0.084 ? ? ? ? ? ? ? ? 3.671 ? ? ? ? 0.098 ? ? 13 1 0.991 ? ? ? ? ? ? ? ? ? ? 2.530 2.740 ? 17.200 ? 2957 811 ? 792 97.700 ? ? ? ? 0.080 ? ? ? ? ? ? ? ? 3.734 ? ? ? ? 0.094 ? ? 14 1 0.991 ? ? ? ? ? ? ? ? ? ? 2.740 3.000 ? 18.610 ? 2695 740 ? 721 97.400 ? ? ? ? 0.063 ? ? ? ? ? ? ? ? 3.738 ? ? ? ? 0.074 ? ? 15 1 0.995 ? ? ? ? ? ? ? ? ? ? 3.000 3.350 ? 19.800 ? 2414 665 ? 659 99.100 ? ? ? ? 0.065 ? ? ? ? ? ? ? ? 3.663 ? ? ? ? 0.076 ? ? 16 1 0.990 ? ? ? ? ? ? ? ? ? ? 3.350 3.870 ? 20.180 ? 2163 602 ? 591 98.200 ? ? ? ? 0.056 ? ? ? ? ? ? ? ? 3.660 ? ? ? ? 0.065 ? ? 17 1 0.997 ? ? ? ? ? ? ? ? ? ? 3.870 4.740 ? 21.340 ? 1754 480 ? 475 99.000 ? ? ? ? 0.053 ? ? ? ? ? ? ? ? 3.693 ? ? ? ? 0.063 ? ? 18 1 0.994 ? ? ? ? ? ? ? ? ? ? 4.740 6.700 ? 21.570 ? 1366 385 ? 380 98.700 ? ? ? ? 0.052 ? ? ? ? ? ? ? ? 3.595 ? ? ? ? 0.062 ? ? 19 1 0.995 ? ? ? ? ? ? ? ? ? ? 6.700 29.250 ? 21.160 ? 645 211 ? 200 94.800 ? ? ? ? 0.053 ? ? ? ? ? ? ? ? 3.225 ? ? ? ? 0.064 ? ? 20 1 0.994 ? ? ? ? ? ? ? ? ? ? # _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 34.260 _refine.B_iso_mean 13.9295 _refine.B_iso_min 6.560 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details 'The entry contains friedel pairs in F_plus/minus columns' _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 7Y8P _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 1.5000 _refine.ls_d_res_low 29.2500 _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 18383 _refine.ls_number_reflns_R_free 1827 _refine.ls_number_reflns_R_work 16556 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.4400 _refine.ls_percent_reflns_R_free 9.9400 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1634 _refine.ls_R_factor_R_free 0.1986 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1596 _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 1.440 _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 5ay2 _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 20.9500 _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 0.1600 _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 1.5000 _refine_hist.d_res_low 29.2500 _refine_hist.number_atoms_solvent 124 _refine_hist.number_atoms_total 658 _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 18.28 _refine_hist.pdbx_B_iso_mean_solvent 21.35 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 506 _refine_hist.pdbx_number_atoms_ligand 28 _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 _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 'X-RAY DIFFRACTION' 1.5000 1.5400 1338 . 135 1203 95.0000 . . . 0.2499 0.0000 0.2295 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.5400 1.5800 1468 . 142 1326 99.0000 . . . 0.3099 0.0000 0.2091 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.5800 1.6400 1375 . 136 1239 99.0000 . . . 0.2422 0.0000 0.1865 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.6400 1.6900 1437 . 148 1289 99.0000 . . . 0.2870 0.0000 0.1868 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.6900 1.7600 1400 . 147 1253 99.0000 . . . 0.2236 0.0000 0.1850 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.7600 1.8400 1438 . 149 1289 99.0000 . . . 0.2397 0.0000 0.1959 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.8400 1.9400 1445 . 137 1308 99.0000 . . . 0.2108 0.0000 0.1862 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.9400 2.0600 1397 . 142 1255 98.0000 . . . 0.1961 0.0000 0.1603 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 2.0600 2.2200 1413 . 136 1277 99.0000 . . . 0.1741 0.0000 0.1634 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 2.2200 2.4400 1435 . 146 1289 100.0000 . . . 0.1839 0.0000 0.1523 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 2.4400 2.8000 1405 . 139 1266 99.0000 . . . 0.1989 0.0000 0.1573 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 2.8000 3.5200 1415 . 140 1275 98.0000 . . . 0.2003 0.0000 0.1308 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 3.5200 29.2500 1417 . 130 1287 98.0000 . . . 0.1347 0.0000 0.1248 . . . . . . . 13 . . . # _struct.entry_id 7Y8P _struct.title ;Crystal structure of 4'-selenoRNA duplex ; _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 7Y8P _struct_keywords.text 'RNA, selen' _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 ? E N N 2 ? F N N 3 ? G N N 3 ? # 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 one ? A A 3 "O3'" ? ? ? 1_555 A IKS 4 P ? ? A A 3 A IKS 4 1_555 ? ? ? ? ? ? ? 1.552 ? ? covale2 covale none ? A IKS 4 "O3'" ? ? ? 1_555 A ILK 5 P ? ? A IKS 4 A ILK 5 1_555 ? ? ? ? ? ? ? 1.558 ? ? covale3 covale none ? A ILK 5 "O3'" ? ? ? 1_555 A IKS 6 P ? ? A ILK 5 A IKS 6 1_555 ? ? ? ? ? ? ? 1.564 ? ? covale4 covale one ? A IKS 6 "O3'" ? ? ? 1_555 A G 7 P ? ? A IKS 6 A G 7 1_555 ? ? ? ? ? ? ? 1.558 ? ? covale5 covale one ? B A 3 "O3'" ? ? ? 1_555 B IKS 4 P ? ? B A 3 B IKS 4 1_555 ? ? ? ? ? ? ? 1.560 ? ? covale6 covale none ? B IKS 4 "O3'" ? ? ? 1_555 B ILK 5 P ? ? B IKS 4 B ILK 5 1_555 ? ? ? ? ? ? ? 1.556 ? ? covale7 covale none ? B ILK 5 "O3'" ? ? ? 1_555 B IKS 6 P ? ? B ILK 5 B IKS 6 1_555 ? ? ? ? ? ? ? 1.568 ? ? covale8 covale one ? B IKS 6 "O3'" ? ? ? 1_555 B G 7 P ? ? B IKS 6 B G 7 1_555 ? ? ? ? ? ? ? 1.560 ? ? 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 A 3 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 3 B U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 3 B U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 10 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 10 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 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 ? ? # _atom_sites.entry_id 7Y8P _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] 0.037104 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.016108 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.026242 _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] 0.034194 _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 C CO N O P SE # 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 IKS 4 4 4 IKS UNK A . n A 1 5 ILK 5 5 5 ILK UNK A . n A 1 6 IKS 6 6 6 IKS UNK 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 U 10 10 10 U U 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 IKS 4 4 4 IKS UNK B . n B 1 5 ILK 5 5 5 ILK UNK B . n B 1 6 IKS 6 6 6 IKS UNK 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 U 10 10 10 U U 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_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_ _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 NCO 1 101 1 NCO NCO A . D 2 NCO 1 102 2 NCO NCO A . E 2 NCO 1 101 3 NCO NCO B . F 3 HOH 1 201 98 HOH HOH A . F 3 HOH 2 202 35 HOH HOH A . F 3 HOH 3 203 38 HOH HOH A . F 3 HOH 4 204 66 HOH HOH A . F 3 HOH 5 205 12 HOH HOH A . F 3 HOH 6 206 71 HOH HOH A . F 3 HOH 7 207 87 HOH HOH A . F 3 HOH 8 208 61 HOH HOH A . F 3 HOH 9 209 14 HOH HOH A . F 3 HOH 10 210 101 HOH HOH A . F 3 HOH 11 211 84 HOH HOH A . F 3 HOH 12 212 60 HOH HOH A . F 3 HOH 13 213 113 HOH HOH A . F 3 HOH 14 214 1 HOH HOH A . F 3 HOH 15 215 127 HOH HOH A . F 3 HOH 16 216 37 HOH HOH A . F 3 HOH 17 217 76 HOH HOH A . F 3 HOH 18 218 126 HOH HOH A . F 3 HOH 19 219 16 HOH HOH A . F 3 HOH 20 220 32 HOH HOH A . F 3 HOH 21 221 52 HOH HOH A . F 3 HOH 22 222 23 HOH HOH A . F 3 HOH 23 223 64 HOH HOH A . F 3 HOH 24 224 11 HOH HOH A . F 3 HOH 25 225 4 HOH HOH A . F 3 HOH 26 226 46 HOH HOH A . F 3 HOH 27 227 15 HOH HOH A . F 3 HOH 28 228 42 HOH HOH A . F 3 HOH 29 229 27 HOH HOH A . F 3 HOH 30 230 99 HOH HOH A . F 3 HOH 31 231 130 HOH HOH A . F 3 HOH 32 232 18 HOH HOH A . F 3 HOH 33 233 34 HOH HOH A . F 3 HOH 34 234 110 HOH HOH A . F 3 HOH 35 235 56 HOH HOH A . F 3 HOH 36 236 40 HOH HOH A . F 3 HOH 37 237 49 HOH HOH A . F 3 HOH 38 238 119 HOH HOH A . F 3 HOH 39 239 3 HOH HOH A . F 3 HOH 40 240 69 HOH HOH A . F 3 HOH 41 241 19 HOH HOH A . F 3 HOH 42 242 7 HOH HOH A . F 3 HOH 43 243 36 HOH HOH A . F 3 HOH 44 244 133 HOH HOH A . F 3 HOH 45 245 43 HOH HOH A . F 3 HOH 46 246 39 HOH HOH A . F 3 HOH 47 247 103 HOH HOH A . F 3 HOH 48 248 81 HOH HOH A . F 3 HOH 49 249 120 HOH HOH A . F 3 HOH 50 250 109 HOH HOH A . F 3 HOH 51 251 33 HOH HOH A . F 3 HOH 52 252 115 HOH HOH A . F 3 HOH 53 253 2 HOH HOH A . F 3 HOH 54 254 90 HOH HOH A . F 3 HOH 55 255 72 HOH HOH A . F 3 HOH 56 256 58 HOH HOH A . F 3 HOH 57 257 48 HOH HOH A . F 3 HOH 58 258 29 HOH HOH A . F 3 HOH 59 259 6 HOH HOH A . F 3 HOH 60 260 97 HOH HOH A . F 3 HOH 61 261 5 HOH HOH A . F 3 HOH 62 262 67 HOH HOH A . F 3 HOH 63 263 129 HOH HOH A . F 3 HOH 64 264 131 HOH HOH A . F 3 HOH 65 265 92 HOH HOH A . F 3 HOH 66 266 107 HOH HOH A . F 3 HOH 67 267 136 HOH HOH A . F 3 HOH 68 268 111 HOH HOH A . G 3 HOH 1 201 125 HOH HOH B . G 3 HOH 2 202 47 HOH HOH B . G 3 HOH 3 203 57 HOH HOH B . G 3 HOH 4 204 82 HOH HOH B . G 3 HOH 5 205 96 HOH HOH B . G 3 HOH 6 206 95 HOH HOH B . G 3 HOH 7 207 41 HOH HOH B . G 3 HOH 8 208 102 HOH HOH B . G 3 HOH 9 209 68 HOH HOH B . G 3 HOH 10 210 73 HOH HOH B . G 3 HOH 11 211 28 HOH HOH B . G 3 HOH 12 212 100 HOH HOH B . G 3 HOH 13 213 10 HOH HOH B . G 3 HOH 14 214 25 HOH HOH B . G 3 HOH 15 215 17 HOH HOH B . G 3 HOH 16 216 78 HOH HOH B . G 3 HOH 17 217 94 HOH HOH B . G 3 HOH 18 218 13 HOH HOH B . G 3 HOH 19 219 9 HOH HOH B . G 3 HOH 20 220 54 HOH HOH B . G 3 HOH 21 221 79 HOH HOH B . G 3 HOH 22 222 30 HOH HOH B . G 3 HOH 23 223 123 HOH HOH B . G 3 HOH 24 224 74 HOH HOH B . G 3 HOH 25 225 128 HOH HOH B . G 3 HOH 26 226 121 HOH HOH B . G 3 HOH 27 227 44 HOH HOH B . G 3 HOH 28 228 50 HOH HOH B . G 3 HOH 29 229 77 HOH HOH B . G 3 HOH 30 230 26 HOH HOH B . G 3 HOH 31 231 86 HOH HOH B . G 3 HOH 32 232 124 HOH HOH B . G 3 HOH 33 233 63 HOH HOH B . G 3 HOH 34 234 122 HOH HOH B . G 3 HOH 35 235 53 HOH HOH B . G 3 HOH 36 236 132 HOH HOH B . G 3 HOH 37 237 65 HOH HOH B . G 3 HOH 38 238 105 HOH HOH B . G 3 HOH 39 239 31 HOH HOH B . G 3 HOH 40 240 89 HOH HOH B . G 3 HOH 41 241 88 HOH HOH B . G 3 HOH 42 242 20 HOH HOH B . G 3 HOH 43 243 51 HOH HOH B . G 3 HOH 44 244 24 HOH HOH B . G 3 HOH 45 245 80 HOH HOH B . G 3 HOH 46 246 8 HOH HOH B . G 3 HOH 47 247 116 HOH HOH B . G 3 HOH 48 248 22 HOH HOH B . G 3 HOH 49 249 85 HOH HOH B . G 3 HOH 50 250 21 HOH HOH B . G 3 HOH 51 251 55 HOH HOH B . G 3 HOH 52 252 70 HOH HOH B . G 3 HOH 53 253 75 HOH HOH B . G 3 HOH 54 254 106 HOH HOH B . G 3 HOH 55 255 135 HOH HOH B . # _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 # _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,E,F,G # 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)' 1740 ? 1 MORE -8 ? 1 'SSA (A^2)' 4700 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2023-05-03 2 'Structure model' 1 1 2023-11-29 # _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' 'Refinement description' # 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' pdbx_initial_refinement_model # 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 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.27 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 5 # _pdbx_entry_details.entry_id 7Y8P _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 1 "O3'" A A 3 ? ? P A IKS 4 ? ? OP2 A IKS 4 ? ? 118.07 110.50 7.57 1.10 Y 2 1 "O3'" A ILK 5 ? ? P A IKS 6 ? ? OP2 A IKS 6 ? ? 119.68 110.50 9.18 1.10 Y 3 1 C8 B G 2 ? ? N9 B G 2 ? ? C4 B G 2 ? ? 110.12 106.40 3.72 0.40 N 4 1 "C3'" B ILK 5 ? ? "O3'" B ILK 5 ? ? P B IKS 6 ? ? 127.43 119.70 7.73 1.20 Y # 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 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 IKS P P N N 114 IKS OP1 O N N 115 IKS OP2 O N N 116 IKS "O5'" O N N 117 IKS "C5'" C N N 118 IKS "C4'" C N R 119 IKS "C3'" C N S 120 IKS "O3'" O N N 121 IKS "C2'" C N R 122 IKS "O2'" O N N 123 IKS "C1'" C N R 124 IKS N1 N N N 125 IKS C2 C N N 126 IKS O2 O N N 127 IKS N3 N N N 128 IKS C4 C N N 129 IKS N4 N N N 130 IKS C5 C N N 131 IKS C6 C N N 132 IKS SE4 SE N N 133 IKS H2 H N N 134 IKS H3 H N N 135 IKS H4 H N N 136 IKS H5 H N N 137 IKS H6 H N N 138 IKS H7 H N N 139 IKS H8 H N N 140 IKS H9 H N N 141 IKS H10 H N N 142 IKS H11 H N N 143 IKS H12 H N N 144 IKS H13 H N N 145 IKS H14 H N N 146 IKS OP3 O N N 147 IKS H1 H N N 148 ILK "C1'" C N R 149 ILK C2 C N N 150 ILK "C2'" C N R 151 ILK "C3'" C N S 152 ILK C4 C N N 153 ILK "C4'" C N R 154 ILK C5 C N N 155 ILK "C5'" C N N 156 ILK C6 C N N 157 ILK N1 N N N 158 ILK N3 N N N 159 ILK O2 O N N 160 ILK "O2'" O N N 161 ILK "O3'" O N N 162 ILK O4 O N N 163 ILK "O5'" O N N 164 ILK OP1 O N N 165 ILK OP2 O N N 166 ILK P P N N 167 ILK SE4 SE N N 168 ILK H1 H N N 169 ILK H2 H N N 170 ILK H3 H N N 171 ILK H4 H N N 172 ILK H5 H N N 173 ILK H6 H N N 174 ILK H7 H N N 175 ILK H8 H N N 176 ILK H9 H N N 177 ILK H10 H N N 178 ILK H11 H N N 179 ILK H13 H N N 180 ILK OP3 O N N 181 ILK H12 H N N 182 NCO CO CO N N 183 NCO N1 N N N 184 NCO N2 N N N 185 NCO N3 N N N 186 NCO N4 N N N 187 NCO N5 N N N 188 NCO N6 N N N 189 NCO HN11 H N N 190 NCO HN12 H N N 191 NCO HN13 H N N 192 NCO HN21 H N N 193 NCO HN22 H N N 194 NCO HN23 H N N 195 NCO HN31 H N N 196 NCO HN32 H N N 197 NCO HN33 H N N 198 NCO HN41 H N N 199 NCO HN42 H N N 200 NCO HN43 H N N 201 NCO HN51 H N N 202 NCO HN52 H N N 203 NCO HN53 H N N 204 NCO HN61 H N N 205 NCO HN62 H N N 206 NCO HN63 H N N 207 U OP3 O N N 208 U P P N N 209 U OP1 O N N 210 U OP2 O N N 211 U "O5'" O N N 212 U "C5'" C N N 213 U "C4'" C N R 214 U "O4'" O N N 215 U "C3'" C N S 216 U "O3'" O N N 217 U "C2'" C N R 218 U "O2'" O N N 219 U "C1'" C N R 220 U N1 N N N 221 U C2 C N N 222 U O2 O N N 223 U N3 N N N 224 U C4 C N N 225 U O4 O N N 226 U C5 C N N 227 U C6 C N N 228 U HOP3 H N N 229 U HOP2 H N N 230 U "H5'" H N N 231 U "H5''" H N N 232 U "H4'" H N N 233 U "H3'" H N N 234 U "HO3'" H N N 235 U "H2'" H N N 236 U "HO2'" H N N 237 U "H1'" H N N 238 U H3 H N N 239 U H5 H N N 240 U H6 H N N 241 # 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 HOH O H1 sing N N 116 HOH O H2 sing N N 117 IKS SE4 "C1'" sing N N 118 IKS SE4 "C4'" sing N N 119 IKS O2 C2 doub N N 120 IKS "C1'" N1 sing N N 121 IKS "C1'" "C2'" sing N N 122 IKS C2 N1 sing N N 123 IKS C2 N3 sing N N 124 IKS N1 C6 sing N N 125 IKS "O2'" "C2'" sing N N 126 IKS "C4'" "C5'" sing N N 127 IKS "C4'" "C3'" sing N N 128 IKS N3 C4 doub N N 129 IKS "C2'" "C3'" sing N N 130 IKS C6 C5 doub N N 131 IKS "C5'" "O5'" sing N N 132 IKS C4 C5 sing N N 133 IKS C4 N4 sing N N 134 IKS "O5'" P sing N N 135 IKS "C3'" "O3'" sing N N 136 IKS P OP1 doub N N 137 IKS P OP2 sing N N 138 IKS OP2 H2 sing N N 139 IKS "C5'" H3 sing N N 140 IKS "C5'" H4 sing N N 141 IKS "C4'" H5 sing N N 142 IKS "C3'" H6 sing N N 143 IKS "O3'" H7 sing N N 144 IKS "C2'" H8 sing N N 145 IKS "O2'" H9 sing N N 146 IKS "C1'" H10 sing N N 147 IKS N4 H11 sing N N 148 IKS N4 H12 sing N N 149 IKS C5 H13 sing N N 150 IKS C6 H14 sing N N 151 IKS P OP3 sing N N 152 IKS OP3 H1 sing N N 153 ILK SE4 "C1'" sing N N 154 ILK SE4 "C4'" sing N N 155 ILK "C1'" N1 sing N N 156 ILK "C1'" "C2'" sing N N 157 ILK "C4'" "C5'" sing N N 158 ILK "C4'" "C3'" sing N N 159 ILK N1 C6 sing N N 160 ILK N1 C2 sing N N 161 ILK O2 C2 doub N N 162 ILK C6 C5 doub N N 163 ILK "C5'" "O5'" sing N N 164 ILK "O2'" "C2'" sing N N 165 ILK C2 N3 sing N N 166 ILK C5 C4 sing N N 167 ILK "O5'" P sing N N 168 ILK N3 C4 sing N N 169 ILK "C2'" "C3'" sing N N 170 ILK C4 O4 doub N N 171 ILK P OP2 sing N N 172 ILK P OP1 doub N N 173 ILK "C3'" "O3'" sing N N 174 ILK "C1'" H1 sing N N 175 ILK "C2'" H2 sing N N 176 ILK "C3'" H3 sing N N 177 ILK "C4'" H4 sing N N 178 ILK C5 H5 sing N N 179 ILK "C5'" H6 sing N N 180 ILK "C5'" H7 sing N N 181 ILK C6 H8 sing N N 182 ILK N3 H9 sing N N 183 ILK "O2'" H10 sing N N 184 ILK "O3'" H11 sing N N 185 ILK OP2 H13 sing N N 186 ILK P OP3 sing N N 187 ILK OP3 H12 sing N N 188 NCO CO N1 sing N N 189 NCO CO N2 sing N N 190 NCO CO N3 sing N N 191 NCO CO N4 sing N N 192 NCO CO N5 sing N N 193 NCO CO N6 sing N N 194 NCO N1 HN11 sing N N 195 NCO N1 HN12 sing N N 196 NCO N1 HN13 sing N N 197 NCO N2 HN21 sing N N 198 NCO N2 HN22 sing N N 199 NCO N2 HN23 sing N N 200 NCO N3 HN31 sing N N 201 NCO N3 HN32 sing N N 202 NCO N3 HN33 sing N N 203 NCO N4 HN41 sing N N 204 NCO N4 HN42 sing N N 205 NCO N4 HN43 sing N N 206 NCO N5 HN51 sing N N 207 NCO N5 HN52 sing N N 208 NCO N5 HN53 sing N N 209 NCO N6 HN61 sing N N 210 NCO N6 HN62 sing N N 211 NCO N6 HN63 sing N N 212 U OP3 P sing N N 213 U OP3 HOP3 sing N N 214 U P OP1 doub N N 215 U P OP2 sing N N 216 U P "O5'" sing N N 217 U OP2 HOP2 sing N N 218 U "O5'" "C5'" sing N N 219 U "C5'" "C4'" sing N N 220 U "C5'" "H5'" sing N N 221 U "C5'" "H5''" sing N N 222 U "C4'" "O4'" sing N N 223 U "C4'" "C3'" sing N N 224 U "C4'" "H4'" sing N N 225 U "O4'" "C1'" sing N N 226 U "C3'" "O3'" sing N N 227 U "C3'" "C2'" sing N N 228 U "C3'" "H3'" sing N N 229 U "O3'" "HO3'" sing N N 230 U "C2'" "O2'" sing N N 231 U "C2'" "C1'" sing N N 232 U "C2'" "H2'" sing N N 233 U "O2'" "HO2'" sing N N 234 U "C1'" N1 sing N N 235 U "C1'" "H1'" sing N N 236 U N1 C2 sing N N 237 U N1 C6 sing N N 238 U C2 O2 doub N N 239 U C2 N3 sing N N 240 U N3 C4 sing N N 241 U N3 H3 sing N N 242 U C4 O4 doub N N 243 U C4 C5 sing N N 244 U C5 C6 doub N N 245 U C5 H5 sing N N 246 U C6 H6 sing N N 247 # _ndb_struct_conf_na.entry_id 7Y8P _ndb_struct_conf_na.feature '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 -0.284 -0.184 0.103 -0.472 -6.349 -2.421 1 A_G1:C12_B A 1 ? B 12 ? 19 1 1 A G 2 1_555 B C 11 1_555 -0.266 -0.211 0.124 3.239 -9.806 -1.586 2 A_G2:C11_B A 2 ? B 11 ? 19 1 1 A A 3 1_555 B U 10 1_555 0.081 -0.127 0.097 3.182 -20.565 3.272 3 A_A3:U10_B A 3 ? B 10 ? 20 1 1 A U 10 1_555 B A 3 1_555 -0.075 -0.161 0.057 3.127 -17.044 -4.852 4 A_U10:A3_B A 10 ? B 3 ? 20 1 1 A C 11 1_555 B G 2 1_555 0.155 -0.173 0.169 4.305 -19.534 1.768 5 A_C11:G2_B A 11 ? B 2 ? 19 1 1 A C 12 1_555 B G 1 1_555 0.154 -0.196 0.297 -0.159 -10.294 -1.881 6 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 -0.632 -1.492 3.131 -3.204 4.764 32.880 -3.337 0.604 2.939 8.336 5.607 33.364 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 A 3 1_555 B U 10 1_555 0.779 -1.375 3.179 1.826 6.352 32.580 -3.403 -1.075 2.904 11.180 -3.213 33.226 2 AA_G2A3:U10C11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A U 10 1_555 B A 3 1_555 A C 11 1_555 B G 2 1_555 1.199 -0.955 3.109 2.848 6.865 35.664 -2.424 -1.548 2.964 11.060 -4.588 36.405 3 AA_U10C11:G2A3_BB A 10 ? B 3 ? 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 0.125 -1.260 3.336 0.051 4.011 37.154 -2.495 -0.189 3.188 6.272 -0.080 37.363 4 AA_C11C12:G1G2_BB A 11 ? B 2 ? A 12 ? B 1 ? # _pdbx_audit_support.funding_organization 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 18H02108 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT HEXAMMINE(III)' NCO 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 5AY2 _pdbx_initial_refinement_model.details ? # _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 ? #