data_5XZ1 # _entry.id 5XZ1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 5XZ1 pdb_00005xz1 10.2210/pdb5xz1/pdb WWPDB D_1300004408 ? ? # 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 2018-07-18 2 'Structure model' 1 1 2024-03-27 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5XZ1 _pdbx_database_status.recvd_initial_deposition_date 2017-07-11 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kanazawa, H.' 1 ? 'Tsurumi, N.' 2 ? 'Kondo, J.' 3 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Structural studies of aminoglycoside antibiotics G418 and its derivatives with readthrough activities' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kanazawa, H.' 1 ? primary 'Tsurumi, N.' 2 ? primary 'Baasov, T.' 3 ? primary 'Kondo, J.' 4 ? # 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(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') ; 7049.243 4 ? ? ? ? 2 non-polymer syn GENETICIN 496.552 4 ? ? ? ? 3 water nat water 18.015 25 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UGCGUCGCUCCGGAAAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can UGCGUCGCUCCGGAAAAGUCGC _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GENETICIN GET 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 G n 1 3 C n 1 4 G n 1 5 U n 1 6 C n 1 7 G n 1 8 C n 1 9 U n 1 10 C n 1 11 C n 1 12 G n 1 13 G n 1 14 A n 1 15 A n 1 16 A n 1 17 A n 1 18 G n 1 19 U n 1 20 C n 1 21 G n 1 22 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 22 _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 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 GET non-polymer . GENETICIN G418 'C20 H40 N4 O10' 496.552 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 U 1 2 2 U U A . n A 1 2 G 2 3 3 G G A . n A 1 3 C 3 4 4 C C A . n A 1 4 G 4 5 5 G G A . n A 1 5 U 5 6 6 U U A . n A 1 6 C 6 7 7 C C A . n A 1 7 G 7 8 8 G G A . n A 1 8 C 8 9 9 C C A . n A 1 9 U 9 10 10 U U A . n A 1 10 C 10 11 11 C C A . n A 1 11 C 11 12 12 C C A . n A 1 12 G 12 13 13 G G A . n A 1 13 G 13 14 14 G G A . n A 1 14 A 14 15 15 A A A . n A 1 15 A 15 16 16 A A A . n A 1 16 A 16 17 17 A A A . n A 1 17 A 17 18 18 A A A . n A 1 18 G 18 19 19 G G A . n A 1 19 U 19 20 20 U U A . n A 1 20 C 20 21 21 C C A . n A 1 21 G 21 22 22 G G A . n A 1 22 C 22 23 23 C C A . n B 1 1 U 1 25 25 U U B . n B 1 2 G 2 26 26 G G B . n B 1 3 C 3 27 27 C C B . n B 1 4 G 4 28 28 G G B . n B 1 5 U 5 29 29 U U B . n B 1 6 C 6 30 30 C C B . n B 1 7 G 7 31 31 G G B . n B 1 8 C 8 32 32 C C B . n B 1 9 U 9 33 33 U U B . n B 1 10 C 10 34 34 C C B . n B 1 11 C 11 35 35 C C B . n B 1 12 G 12 36 36 G G B . n B 1 13 G 13 37 37 G G B . n B 1 14 A 14 38 38 A A B . n B 1 15 A 15 39 39 A A B . n B 1 16 A 16 40 40 A A B . n B 1 17 A 17 41 41 A A B . n B 1 18 G 18 42 42 G G B . n B 1 19 U 19 43 43 U U B . n B 1 20 C 20 44 44 C C B . n B 1 21 G 21 45 45 G G B . n B 1 22 C 22 46 46 C C B . n C 1 1 U 1 48 48 U U C . n C 1 2 G 2 49 49 G G C . n C 1 3 C 3 50 50 C C C . n C 1 4 G 4 51 51 G G C . n C 1 5 U 5 52 52 U U C . n C 1 6 C 6 53 53 C C C . n C 1 7 G 7 54 54 G G C . n C 1 8 C 8 55 55 C C C . n C 1 9 U 9 56 56 U U C . n C 1 10 C 10 57 57 C C C . n C 1 11 C 11 58 58 C C C . n C 1 12 G 12 59 59 G G C . n C 1 13 G 13 60 60 G G C . n C 1 14 A 14 61 61 A A C . n C 1 15 A 15 62 62 A A C . n C 1 16 A 16 63 63 A A C . n C 1 17 A 17 64 64 A A C . n C 1 18 G 18 65 65 G G C . n C 1 19 U 19 66 66 U U C . n C 1 20 C 20 67 67 C C C . n C 1 21 G 21 68 68 G G C . n C 1 22 C 22 69 69 C C C . n D 1 1 U 1 71 71 U U D . n D 1 2 G 2 72 72 G G D . n D 1 3 C 3 73 73 C C D . n D 1 4 G 4 74 74 G G D . n D 1 5 U 5 75 75 U U D . n D 1 6 C 6 76 76 C C D . n D 1 7 G 7 77 77 G G D . n D 1 8 C 8 78 78 C C D . n D 1 9 U 9 79 79 U U D . n D 1 10 C 10 80 80 C C D . n D 1 11 C 11 81 81 C C D . n D 1 12 G 12 82 82 G G D . n D 1 13 G 13 83 83 G G D . n D 1 14 A 14 84 84 A A D . n D 1 15 A 15 85 85 A A D . n D 1 16 A 16 86 86 A A D . n D 1 17 A 17 87 87 A A D . n D 1 18 G 18 88 88 G G D . n D 1 19 U 19 89 89 U U D . n D 1 20 C 20 90 90 C C D . n D 1 21 G 21 91 91 G G D . n D 1 22 C 22 92 92 C C D . n # 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 E 2 GET 1 101 304 GET GET A . F 2 GET 1 301 301 GET GET B . G 2 GET 1 101 302 GET GET C . H 2 GET 1 102 303 GET GET C . I 3 HOH 1 201 125 HOH HOH A . I 3 HOH 2 202 112 HOH HOH A . I 3 HOH 3 203 108 HOH HOH A . I 3 HOH 4 204 124 HOH HOH A . J 3 HOH 1 401 111 HOH HOH B . J 3 HOH 2 402 109 HOH HOH B . J 3 HOH 3 403 120 HOH HOH B . J 3 HOH 4 404 113 HOH HOH B . J 3 HOH 5 405 104 HOH HOH B . J 3 HOH 6 406 123 HOH HOH B . J 3 HOH 7 407 106 HOH HOH B . J 3 HOH 8 408 105 HOH HOH B . K 3 HOH 1 201 114 HOH HOH C . K 3 HOH 2 202 118 HOH HOH C . K 3 HOH 3 203 107 HOH HOH C . K 3 HOH 4 204 110 HOH HOH C . K 3 HOH 5 205 117 HOH HOH C . K 3 HOH 6 206 115 HOH HOH C . K 3 HOH 7 207 121 HOH HOH C . K 3 HOH 8 208 116 HOH HOH C . K 3 HOH 9 209 102 HOH HOH C . L 3 HOH 1 101 119 HOH HOH D . L 3 HOH 2 102 101 HOH HOH D . L 3 HOH 3 103 122 HOH HOH D . L 3 HOH 4 104 103 HOH HOH D . # 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 ? ? ? 1.8.3_1479 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.22 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 4 # _cell.length_a 47.399 _cell.length_b 32.528 _cell.length_c 96.484 _cell.angle_alpha 90.000 _cell.angle_beta 95.580 _cell.angle_gamma 90.000 _cell.entry_id 5XZ1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.entry_id 5XZ1 _symmetry.Int_Tables_number 4 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? # _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 5XZ1 _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 2.63 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 53.15 _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_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 '2-methyl-2,4-pentandiol, Sodium cacodylate, Spermine tetrahydrochloride' _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_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 2M-F' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-06-23 # _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.entry_id 5XZ1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 48.013 _reflns.d_resolution_high 3.010 _reflns.number_obs 5988 _reflns.number_all ? _reflns.percent_possible_obs 98.500 _reflns.pdbx_Rmerge_I_obs 0.070 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 12.460 _reflns.B_iso_Wilson_estimate 54.560 _reflns.pdbx_redundancy 3.285 _reflns.pdbx_Rrim_I_all 0.084 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_CC_half 0.998 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_number_measured_all 19672 _reflns.pdbx_scaling_rejects 32 _reflns.pdbx_chi_squared 0.910 _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.details ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_CC_half 1 1 3.010 3.090 1238 ? 412 ? 0.356 2.530 ? ? 3.005 ? ? 430 ? ? ? ? ? 95.800 0.428 ? 0.921 1 2 3.090 3.170 1439 ? 436 ? 0.196 4.370 ? ? 3.300 ? ? 438 ? ? ? ? ? 99.500 0.234 ? 0.984 1 3 3.170 3.260 1374 ? 405 ? 0.185 4.900 ? ? 3.393 ? ? 412 ? ? ? ? ? 98.300 0.220 ? 0.987 1 4 3.260 3.360 1392 ? 404 ? 0.129 6.620 ? ? 3.446 ? ? 406 ? ? ? ? ? 99.500 0.154 ? 0.992 1 5 3.360 3.470 1267 ? 382 ? 0.179 6.080 ? ? 3.317 ? ? 388 ? ? ? ? ? 98.500 0.214 ? 0.981 1 6 3.470 3.600 1354 ? 407 ? 0.108 8.050 ? ? 3.327 ? ? 412 ? ? ? ? ? 98.800 0.130 ? 0.993 1 7 3.600 3.730 1088 ? 341 ? 0.101 8.880 ? ? 3.191 ? ? 351 ? ? ? ? ? 97.200 0.122 ? 0.994 1 8 3.730 3.880 1142 ? 353 ? 0.085 9.580 ? ? 3.235 ? ? 357 ? ? ? ? ? 98.900 0.103 ? 0.997 1 9 3.880 4.060 977 ? 337 ? 0.084 10.570 ? ? 2.899 ? ? 350 ? ? ? ? ? 96.300 0.101 ? 0.993 1 10 4.060 4.250 1059 ? 318 ? 0.074 13.310 ? ? 3.330 ? ? 322 ? ? ? ? ? 98.800 0.087 ? 0.994 1 11 4.250 4.480 1125 ? 317 ? 0.065 16.610 ? ? 3.549 ? ? 321 ? ? ? ? ? 98.800 0.077 ? 0.995 1 12 4.480 4.760 1051 ? 302 ? 0.062 17.180 ? ? 3.480 ? ? 307 ? ? ? ? ? 98.400 0.074 ? 0.995 1 13 4.760 5.090 930 ? 264 ? 0.056 19.170 ? ? 3.523 ? ? 264 ? ? ? ? ? 100.000 0.066 ? 0.996 1 14 5.090 5.490 921 ? 271 ? 0.048 22.420 ? ? 3.399 ? ? 273 ? ? ? ? ? 99.300 0.058 ? 0.993 1 15 5.490 6.020 821 ? 239 ? 0.042 22.740 ? ? 3.435 ? ? 241 ? ? ? ? ? 99.200 0.050 ? 0.996 1 16 6.020 6.730 764 ? 223 ? 0.042 22.240 ? ? 3.426 ? ? 226 ? ? ? ? ? 98.700 0.050 ? 0.998 1 17 6.730 7.770 617 ? 192 ? 0.037 25.470 ? ? 3.214 ? ? 192 ? ? ? ? ? 100.000 0.045 ? 0.996 1 18 7.770 9.510 530 ? 172 ? 0.037 25.690 ? ? 3.081 ? ? 172 ? ? ? ? ? 100.000 0.045 ? 0.997 1 19 9.510 13.450 401 ? 132 ? 0.030 29.030 ? ? 3.038 ? ? 134 ? ? ? ? ? 98.500 0.037 ? 0.998 1 20 13.450 48.013 182 ? 81 ? 0.031 25.840 ? ? 2.247 ? ? 85 ? ? ? ? ? 95.300 0.038 ? 0.999 # _refine.entry_id 5XZ1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 3.0080 _refine.ls_d_res_low 48.0130 _refine.pdbx_ls_sigma_F 1.350 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 97.8600 _refine.ls_number_reflns_obs 5949 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.193 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.199 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 9.5500 _refine.ls_number_reflns_R_free 568 _refine.ls_number_reflns_R_work 5381 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 59.1300 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.3200 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8176 _refine.B_iso_max 123.050 _refine.B_iso_min 33.050 _refine.pdbx_overall_phase_error 23.8000 _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 3.0080 _refine_hist.d_res_low 48.0130 _refine_hist.pdbx_number_atoms_ligand 136 _refine_hist.number_atoms_solvent 25 _refine_hist.number_atoms_total 2025 _refine_hist.pdbx_number_residues_total 88 _refine_hist.pdbx_B_iso_mean_ligand 56.52 _refine_hist.pdbx_B_iso_mean_solvent 50.19 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1864 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' f_bond_d 2224 0.018 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 3456 1.348 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 496 0.667 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 88 0.020 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 1044 15.700 ? ? ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.R_factor_obs 3.0085 3.3112 4 97.0000 1298 . 0.2649 0.2775 . 139 0.0000 1437 . 'X-RAY DIFFRACTION' . 3.3112 3.7901 4 97.0000 1302 . 0.2033 0.2185 . 147 0.0000 1449 . 'X-RAY DIFFRACTION' . 3.7901 4.7745 4 98.0000 1366 . 0.1805 0.1985 . 139 0.0000 1505 . 'X-RAY DIFFRACTION' . 4.7745 48.0194 4 99.0000 1415 . 0.1719 0.1668 . 143 0.0000 1558 . 'X-RAY DIFFRACTION' . # _struct.entry_id 5XZ1 _struct.title 'Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418' _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 5XZ1 _struct_keywords.text 'ribosome, decoding site, G418, 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 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 3 ? J N N 3 ? K N N 3 ? L N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5XZ1 _struct_ref.pdbx_db_accession 5XZ1 _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 5XZ1 A 1 ? 22 ? 5XZ1 2 ? 23 ? 2 23 2 1 5XZ1 B 1 ? 22 ? 5XZ1 25 ? 46 ? 25 46 3 1 5XZ1 C 1 ? 22 ? 5XZ1 48 ? 69 ? 48 69 4 1 5XZ1 D 1 ? 22 ? 5XZ1 71 ? 92 ? 71 92 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 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)' 3890 ? 1 MORE -45 ? 1 'SSA (A^2)' 8090 ? 2 'ABSA (A^2)' 4110 ? 2 MORE -52 ? 2 'SSA (A^2)' 7840 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,I,J 2 1 C,D,G,H,K,L # _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 hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 22 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 22 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 22 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 21 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 21 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 21 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 O4 ? ? ? 1_555 B U 19 N3 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 18 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 18 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 18 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 8 N4 ? ? ? 1_555 B A 15 N1 ? ? A C 9 B A 39 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog15 hydrog ? ? A U 9 N3 ? ? ? 1_555 B A 14 N1 ? ? A U 10 B A 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 9 O4 ? ? ? 1_555 B A 14 N6 ? ? A U 10 B A 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 14 N1 ? ? ? 1_555 B U 9 N3 ? ? A A 15 B U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 14 N6 ? ? ? 1_555 B U 9 O4 ? ? A A 15 B U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 15 N1 ? ? ? 1_555 B C 8 N4 ? ? A A 16 B C 32 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog32 hydrog ? ? A G 18 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 18 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 18 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A U 19 N3 ? ? ? 1_555 B U 5 O4 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog36 hydrog ? ? A U 19 O2 ? ? ? 1_555 B U 5 N3 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog37 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 21 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 21 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 21 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 22 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 22 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 22 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 22 N3 ? ? C G 49 D C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C G 2 N2 ? ? ? 1_555 D C 22 O2 ? ? C G 49 D C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C G 2 O6 ? ? ? 1_555 D C 22 N4 ? ? C G 49 D C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C C 3 N3 ? ? ? 1_555 D G 21 N1 ? ? C C 50 D G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C C 3 N4 ? ? ? 1_555 D G 21 O6 ? ? C C 50 D G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C C 3 O2 ? ? ? 1_555 D G 21 N2 ? ? C C 50 D G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 20 N3 ? ? C G 51 D C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C G 4 N2 ? ? ? 1_555 D C 20 O2 ? ? C G 51 D C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C G 4 O6 ? ? ? 1_555 D C 20 N4 ? ? C G 51 D C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C U 5 N3 ? ? ? 1_555 D U 19 O2 ? ? C U 52 D U 89 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog56 hydrog ? ? C U 5 O4 ? ? ? 1_555 D U 19 N3 ? ? C U 52 D U 89 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog57 hydrog ? ? C C 6 N3 ? ? ? 1_555 D G 18 N1 ? ? C C 53 D G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C C 6 N4 ? ? ? 1_555 D G 18 O6 ? ? C C 53 D G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C C 6 O2 ? ? ? 1_555 D G 18 N2 ? ? C C 53 D G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C C 8 N4 ? ? ? 1_555 D A 15 N1 ? ? C C 55 D A 85 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog61 hydrog ? ? C U 9 N3 ? ? ? 1_555 D A 14 N1 ? ? C U 56 D A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C U 9 O4 ? ? ? 1_555 D A 14 N6 ? ? C U 56 D A 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C C 10 N3 ? ? ? 1_555 D G 13 N1 ? ? C C 57 D G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C C 10 N4 ? ? ? 1_555 D G 13 O6 ? ? C C 57 D G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? C C 10 O2 ? ? ? 1_555 D G 13 N2 ? ? C C 57 D G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? C C 11 N3 ? ? ? 1_555 D G 12 N1 ? ? C C 58 D G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? C C 11 N4 ? ? ? 1_555 D G 12 O6 ? ? C C 58 D G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? C C 11 O2 ? ? ? 1_555 D G 12 N2 ? ? C C 58 D G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? C G 12 N1 ? ? ? 1_555 D C 11 N3 ? ? C G 59 D C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? C G 12 N2 ? ? ? 1_555 D C 11 O2 ? ? C G 59 D C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? C G 12 O6 ? ? ? 1_555 D C 11 N4 ? ? C G 59 D C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? C G 13 N1 ? ? ? 1_555 D C 10 N3 ? ? C G 60 D C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? C G 13 N2 ? ? ? 1_555 D C 10 O2 ? ? C G 60 D C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? C G 13 O6 ? ? ? 1_555 D C 10 N4 ? ? C G 60 D C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? C A 14 N1 ? ? ? 1_555 D U 9 N3 ? ? C A 61 D U 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? C A 14 N6 ? ? ? 1_555 D U 9 O4 ? ? C A 61 D U 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? C A 15 N1 ? ? ? 1_555 D C 8 N4 ? ? C A 62 D C 78 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog78 hydrog ? ? C G 18 N1 ? ? ? 1_555 D C 6 N3 ? ? C G 65 D C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? C G 18 N2 ? ? ? 1_555 D C 6 O2 ? ? C G 65 D C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? C G 18 O6 ? ? ? 1_555 D C 6 N4 ? ? C G 65 D C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? C U 19 N3 ? ? ? 1_555 D U 5 O4 ? ? C U 66 D U 75 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog82 hydrog ? ? C U 19 O2 ? ? ? 1_555 D U 5 N3 ? ? C U 66 D U 75 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog83 hydrog ? ? C C 20 N3 ? ? ? 1_555 D G 4 N1 ? ? C C 67 D G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? C C 20 N4 ? ? ? 1_555 D G 4 O6 ? ? C C 67 D G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? C C 20 O2 ? ? ? 1_555 D G 4 N2 ? ? C C 67 D G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? C G 21 N1 ? ? ? 1_555 D C 3 N3 ? ? C G 68 D C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? C G 21 N2 ? ? ? 1_555 D C 3 O2 ? ? C G 68 D C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? C G 21 O6 ? ? ? 1_555 D C 3 N4 ? ? C G 68 D C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? C C 22 N3 ? ? ? 1_555 D G 2 N1 ? ? C C 69 D G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? C C 22 N4 ? ? ? 1_555 D G 2 O6 ? ? C C 69 D G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? C C 22 O2 ? ? ? 1_555 D G 2 N2 ? ? C C 69 D G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A GET 101 ? 10 'binding site for residue GET A 101' AC2 Software B GET 301 ? 11 'binding site for residue GET B 301' AC3 Software C GET 101 ? 12 'binding site for residue GET C 101' AC4 Software C GET 102 ? 12 'binding site for residue GET C 102' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 10 A A 15 ? A A 16 . ? 1_555 ? 2 AC1 10 A A 17 ? A A 18 . ? 1_555 ? 3 AC1 10 G A 18 ? G A 19 . ? 1_555 ? 4 AC1 10 U A 19 ? U A 20 . ? 1_555 ? 5 AC1 10 C B 3 ? C B 27 . ? 1_555 ? 6 AC1 10 G B 4 ? G B 28 . ? 1_555 ? 7 AC1 10 U B 5 ? U B 29 . ? 1_555 ? 8 AC1 10 C B 6 ? C B 30 . ? 1_555 ? 9 AC1 10 G B 7 ? G B 31 . ? 1_555 ? 10 AC1 10 C B 8 ? C B 32 . ? 1_555 ? 11 AC2 11 C A 3 ? C A 4 . ? 1_555 ? 12 AC2 11 G A 4 ? G A 5 . ? 1_555 ? 13 AC2 11 U A 5 ? U A 6 . ? 1_555 ? 14 AC2 11 C A 6 ? C A 7 . ? 1_555 ? 15 AC2 11 G A 7 ? G A 8 . ? 1_555 ? 16 AC2 11 C A 8 ? C A 9 . ? 1_555 ? 17 AC2 11 A B 15 ? A B 39 . ? 1_555 ? 18 AC2 11 A B 16 ? A B 40 . ? 1_555 ? 19 AC2 11 A B 17 ? A B 41 . ? 1_555 ? 20 AC2 11 G B 18 ? G B 42 . ? 1_555 ? 21 AC2 11 U B 19 ? U B 43 . ? 1_555 ? 22 AC3 12 U C 1 ? U C 48 . ? 1_555 ? 23 AC3 12 C C 3 ? C C 50 . ? 1_555 ? 24 AC3 12 G C 4 ? G C 51 . ? 1_555 ? 25 AC3 12 U C 5 ? U C 52 . ? 1_555 ? 26 AC3 12 C C 6 ? C C 53 . ? 1_555 ? 27 AC3 12 G C 7 ? G C 54 . ? 1_555 ? 28 AC3 12 C C 8 ? C C 55 . ? 1_555 ? 29 AC3 12 A D 15 ? A D 85 . ? 1_555 ? 30 AC3 12 A D 16 ? A D 86 . ? 1_555 ? 31 AC3 12 A D 17 ? A D 87 . ? 1_555 ? 32 AC3 12 G D 18 ? G D 88 . ? 1_555 ? 33 AC3 12 U D 19 ? U D 89 . ? 1_555 ? 34 AC4 12 U B 1 ? U B 25 . ? 1_655 ? 35 AC4 12 A C 15 ? A C 62 . ? 1_555 ? 36 AC4 12 A C 16 ? A C 63 . ? 1_555 ? 37 AC4 12 A C 17 ? A C 64 . ? 1_555 ? 38 AC4 12 G C 18 ? G C 65 . ? 1_555 ? 39 AC4 12 U C 19 ? U C 66 . ? 1_555 ? 40 AC4 12 C D 3 ? C D 73 . ? 1_555 ? 41 AC4 12 G D 4 ? G D 74 . ? 1_555 ? 42 AC4 12 U D 5 ? U D 75 . ? 1_555 ? 43 AC4 12 C D 6 ? C D 76 . ? 1_555 ? 44 AC4 12 G D 7 ? G D 77 . ? 1_555 ? 45 AC4 12 C D 8 ? C D 78 . ? 1_555 ? # 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 GET C11 C N S 111 GET O11 O N N 112 GET C21 C N R 113 GET N21 N N N 114 GET C31 C N R 115 GET O31 O N N 116 GET C41 C N S 117 GET O41 O N N 118 GET C51 C N R 119 GET O51 O N N 120 GET C61 C N R 121 GET O61 O N N 122 GET C71 C N N 123 GET C12 C N R 124 GET N12 N N N 125 GET C22 C N N 126 GET C32 C N S 127 GET N32 N N N 128 GET C42 C N R 129 GET C52 C N S 130 GET O52 O N N 131 GET C62 C N S 132 GET O62 O N N 133 GET C13 C N R 134 GET C23 C N R 135 GET O23 O N N 136 GET C33 C N R 137 GET N33 N N N 138 GET C93 C N N 139 GET C43 C N R 140 GET O43 O N N 141 GET C83 C N N 142 GET C53 C N N 143 GET O53 O N N 144 GET H111 H N N 145 GET H21 H N N 146 GET H211 H N N 147 GET H212 H N N 148 GET H311 H N N 149 GET H31 H N N 150 GET H411 H N N 151 GET H41 H N N 152 GET H511 H N N 153 GET H611 H N N 154 GET H61 H N N 155 GET H711 H N N 156 GET H712 H N N 157 GET H713 H N N 158 GET H12 H N N 159 GET H121 H N N 160 GET H122 H N N 161 GET H221 H N N 162 GET H222 H N N 163 GET H32 H N N 164 GET H321 H N N 165 GET H322 H N N 166 GET H421 H N N 167 GET H521 H N N 168 GET H52 H N N 169 GET H621 H N N 170 GET H131 H N N 171 GET H231 H N N 172 GET H23 H N N 173 GET H331 H N N 174 GET H33 H N N 175 GET H931 H N N 176 GET H932 H N N 177 GET H933 H N N 178 GET H43 H N N 179 GET H831 H N N 180 GET H832 H N N 181 GET H833 H N N 182 GET H531 H N N 183 GET H532 H N N 184 HOH O O N N 185 HOH H1 H N N 186 HOH H2 H N N 187 U OP3 O N N 188 U P P N N 189 U OP1 O N N 190 U OP2 O N N 191 U "O5'" O N N 192 U "C5'" C N N 193 U "C4'" C N R 194 U "O4'" O N N 195 U "C3'" C N S 196 U "O3'" O N N 197 U "C2'" C N R 198 U "O2'" O N N 199 U "C1'" C N R 200 U N1 N N N 201 U C2 C N N 202 U O2 O N N 203 U N3 N N N 204 U C4 C N N 205 U O4 O N N 206 U C5 C N N 207 U C6 C N N 208 U HOP3 H N N 209 U HOP2 H N N 210 U "H5'" H N N 211 U "H5''" H N N 212 U "H4'" H N N 213 U "H3'" H N N 214 U "HO3'" H N N 215 U "H2'" H N N 216 U "HO2'" H N N 217 U "H1'" H N N 218 U H3 H N N 219 U H5 H N N 220 U H6 H N N 221 # 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 GET C11 O11 sing N N 116 GET C11 C21 sing N N 117 GET C11 O51 sing N N 118 GET C11 H111 sing N N 119 GET O11 C42 sing N N 120 GET C21 N21 sing N N 121 GET C21 C31 sing N N 122 GET C21 H21 sing N N 123 GET N21 H211 sing N N 124 GET N21 H212 sing N N 125 GET C31 O31 sing N N 126 GET C31 C41 sing N N 127 GET C31 H311 sing N N 128 GET O31 H31 sing N N 129 GET C41 O41 sing N N 130 GET C41 C51 sing N N 131 GET C41 H411 sing N N 132 GET O41 H41 sing N N 133 GET C51 O51 sing N N 134 GET C51 C61 sing N N 135 GET C51 H511 sing N N 136 GET C61 O61 sing N N 137 GET C61 C71 sing N N 138 GET C61 H611 sing N N 139 GET O61 H61 sing N N 140 GET C71 H711 sing N N 141 GET C71 H712 sing N N 142 GET C71 H713 sing N N 143 GET C12 N12 sing N N 144 GET C12 C22 sing N N 145 GET C12 C62 sing N N 146 GET C12 H12 sing N N 147 GET N12 H121 sing N N 148 GET N12 H122 sing N N 149 GET C22 C32 sing N N 150 GET C22 H221 sing N N 151 GET C22 H222 sing N N 152 GET C32 N32 sing N N 153 GET C32 C42 sing N N 154 GET C32 H32 sing N N 155 GET N32 H321 sing N N 156 GET N32 H322 sing N N 157 GET C42 C52 sing N N 158 GET C42 H421 sing N N 159 GET C52 O52 sing N N 160 GET C52 C62 sing N N 161 GET C52 H521 sing N N 162 GET O52 H52 sing N N 163 GET C62 O62 sing N N 164 GET C62 H621 sing N N 165 GET O62 C13 sing N N 166 GET C13 C23 sing N N 167 GET C13 O53 sing N N 168 GET C13 H131 sing N N 169 GET C23 O23 sing N N 170 GET C23 C33 sing N N 171 GET C23 H231 sing N N 172 GET O23 H23 sing N N 173 GET C33 N33 sing N N 174 GET C33 C43 sing N N 175 GET C33 H331 sing N N 176 GET N33 C93 sing N N 177 GET N33 H33 sing N N 178 GET C93 H931 sing N N 179 GET C93 H932 sing N N 180 GET C93 H933 sing N N 181 GET C43 O43 sing N N 182 GET C43 C83 sing N N 183 GET C43 C53 sing N N 184 GET O43 H43 sing N N 185 GET C83 H831 sing N N 186 GET C83 H832 sing N N 187 GET C83 H833 sing N N 188 GET C53 O53 sing N N 189 GET C53 H531 sing N N 190 GET C53 H532 sing N N 191 HOH O H1 sing N N 192 HOH O H2 sing N N 193 U OP3 P sing N N 194 U OP3 HOP3 sing N N 195 U P OP1 doub N N 196 U P OP2 sing N N 197 U P "O5'" sing N N 198 U OP2 HOP2 sing N N 199 U "O5'" "C5'" sing N N 200 U "C5'" "C4'" sing N N 201 U "C5'" "H5'" sing N N 202 U "C5'" "H5''" sing N N 203 U "C4'" "O4'" sing N N 204 U "C4'" "C3'" sing N N 205 U "C4'" "H4'" sing N N 206 U "O4'" "C1'" sing N N 207 U "C3'" "O3'" sing N N 208 U "C3'" "C2'" sing N N 209 U "C3'" "H3'" sing N N 210 U "O3'" "HO3'" sing N N 211 U "C2'" "O2'" sing N N 212 U "C2'" "C1'" sing N N 213 U "C2'" "H2'" sing N N 214 U "O2'" "HO2'" sing N N 215 U "C1'" N1 sing N N 216 U "C1'" "H1'" sing N N 217 U N1 C2 sing N N 218 U N1 C6 sing N N 219 U C2 O2 doub N N 220 U C2 N3 sing N N 221 U N3 C4 sing N N 222 U N3 H3 sing N N 223 U C4 O4 doub N N 224 U C4 C5 sing N N 225 U C5 C6 doub N N 226 U C5 H5 sing N N 227 U C6 H6 sing N N 228 # _ndb_struct_conf_na.entry_id 5XZ1 _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 2 1_555 B C 22 1_555 0.096 -0.314 0.256 3.618 -1.548 0.950 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 3 1_555 B G 21 1_555 0.365 -0.313 0.041 4.081 -7.893 2.585 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 4 1_555 B C 20 1_555 -0.299 -0.204 -0.455 -0.283 -8.603 1.007 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A U 5 1_555 B U 19 1_555 -2.341 -1.418 -0.673 5.481 -5.906 -16.710 4 A_U6:U43_B A 6 ? B 43 ? ? ? 1 A C 6 1_555 B G 18 1_555 0.185 -0.126 -0.266 0.733 5.142 -5.383 5 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 8 1_555 B A 15 1_555 -1.056 0.016 0.283 4.879 -13.794 6.766 6 A_C9:A39_B A 9 ? B 39 ? ? 1 1 A U 9 1_555 B A 14 1_555 0.262 -0.492 -0.266 7.934 -15.441 -2.154 7 A_U10:A38_B A 10 ? B 38 ? 20 1 1 A C 10 1_555 B G 13 1_555 -0.148 -0.071 0.130 3.835 -9.679 2.717 8 A_C11:G37_B A 11 ? B 37 ? 19 1 1 A C 11 1_555 B G 12 1_555 0.818 -0.387 -0.124 3.385 -8.131 -4.461 9 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 12 1_555 B C 11 1_555 0.452 -0.353 -0.224 -2.544 -13.318 -0.572 10 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A G 13 1_555 B C 10 1_555 -0.177 -0.148 0.068 -0.270 -11.403 1.726 11 A_G14:C34_B A 14 ? B 34 ? 19 1 1 A A 14 1_555 B U 9 1_555 0.887 -0.227 -0.011 -3.509 -12.276 6.860 12 A_A15:U33_B A 15 ? B 33 ? 20 1 1 A A 15 1_555 B C 8 1_555 1.203 0.081 0.103 -13.862 -17.967 10.763 13 A_A16:C32_B A 16 ? B 32 ? ? 1 1 A G 18 1_555 B C 6 1_555 -0.320 -0.190 -0.284 -3.409 -1.888 -0.759 14 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 19 1_555 B U 5 1_555 1.611 -1.610 -0.121 -6.985 -12.253 -5.173 15 A_U20:U29_B A 20 ? B 29 ? 16 1 1 A C 20 1_555 B G 4 1_555 0.032 -0.280 0.067 3.674 -15.458 3.397 16 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 21 1_555 B C 3 1_555 -0.165 -0.201 0.118 -1.677 -9.982 -1.000 17 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 22 1_555 B G 2 1_555 0.817 -0.135 0.117 8.052 -8.676 2.066 18 A_C23:G26_B A 23 ? B 26 ? 19 1 1 C G 2 1_555 D C 22 1_555 -1.175 -0.418 0.314 -5.311 -7.268 2.773 19 C_G49:C92_D C 49 ? D 92 ? 19 1 1 C C 3 1_555 D G 21 1_555 0.458 -0.260 0.021 2.039 -6.880 -4.643 20 C_C50:G91_D C 50 ? D 91 ? 19 1 1 C G 4 1_555 D C 20 1_555 -0.152 -0.249 -0.104 -4.825 -0.092 1.508 21 C_G51:C90_D C 51 ? D 90 ? 19 1 1 C U 5 1_555 D U 19 1_555 -2.065 -1.628 -0.400 3.873 -7.160 -8.970 22 C_U52:U89_D C 52 ? D 89 ? 16 1 1 C C 6 1_555 D G 18 1_555 0.457 -0.329 -0.290 0.594 -4.084 -2.320 23 C_C53:G88_D C 53 ? D 88 ? 19 1 1 C C 8 1_555 D A 15 1_555 -1.792 0.086 -0.167 10.275 -16.348 4.715 24 C_C55:A85_D C 55 ? D 85 ? ? 1 1 C U 9 1_555 D A 14 1_555 0.452 -0.271 0.124 5.690 -13.860 -1.715 25 C_U56:A84_D C 56 ? D 84 ? 20 1 1 C C 10 1_555 D G 13 1_555 0.987 -0.234 0.334 5.069 -13.348 6.454 26 C_C57:G83_D C 57 ? D 83 ? 19 1 1 C C 11 1_555 D G 12 1_555 -0.078 -0.114 0.022 -1.584 -6.981 0.915 27 C_C58:G82_D C 58 ? D 82 ? 19 1 1 C G 12 1_555 D C 11 1_555 -0.501 -0.047 0.175 -2.425 -12.468 6.591 28 C_G59:C81_D C 59 ? D 81 ? 19 1 1 C G 13 1_555 D C 10 1_555 -0.503 -0.093 0.575 -2.080 -14.312 7.243 29 C_G60:C80_D C 60 ? D 80 ? 19 1 1 C A 14 1_555 D U 9 1_555 0.156 -0.139 0.092 -6.581 -20.064 -0.011 30 C_A61:U79_D C 61 ? D 79 ? 20 1 1 C A 15 1_555 D C 8 1_555 0.559 0.068 0.744 -3.619 -19.710 10.298 31 C_A62:C78_D C 62 ? D 78 ? ? 1 1 C G 18 1_555 D C 6 1_555 -0.708 -0.281 -0.379 2.061 -1.655 -2.146 32 C_G65:C76_D C 65 ? D 76 ? 19 1 1 C U 19 1_555 D U 5 1_555 2.171 -1.642 -0.605 -4.505 -12.468 -11.410 33 C_U66:U75_D C 66 ? D 75 ? 16 1 1 C C 20 1_555 D G 4 1_555 0.429 -0.302 -0.298 5.564 -3.932 5.171 34 C_C67:G74_D C 67 ? D 74 ? 19 1 1 C G 21 1_555 D C 3 1_555 -0.637 -0.398 -0.240 -1.696 -11.391 3.604 35 C_G68:C73_D C 68 ? D 73 ? 19 1 1 C C 22 1_555 D G 2 1_555 -0.114 0.175 0.099 2.275 -7.557 8.774 36 C_C69:G72_D C 69 ? D 72 ? 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 2 1_555 B C 22 1_555 A C 3 1_555 B G 21 1_555 0.031 -1.811 3.253 -0.073 1.793 34.546 -3.317 -0.062 3.158 3.017 0.122 34.592 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 3 1_555 B G 21 1_555 A G 4 1_555 B C 20 1_555 -0.717 -1.639 3.294 4.121 10.869 26.893 -5.362 2.223 2.336 22.104 -8.381 29.255 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 4 1_555 B C 20 1_555 A U 5 1_555 B U 19 1_555 -0.837 -2.057 3.036 -3.679 4.587 24.077 -6.031 0.958 2.698 10.791 8.655 24.774 3 AA_G5U6:U43C44_BB A 5 ? B 44 ? A 6 ? B 43 ? 1 A U 5 1_555 B U 19 1_555 A C 6 1_555 B G 18 1_555 1.260 -2.503 3.681 -0.941 -0.124 43.204 -3.385 -1.814 3.661 -0.168 1.278 43.214 4 AA_U6C7:G42U43_BB A 6 ? B 43 ? A 7 ? B 42 ? 1 A C 8 1_555 B A 15 1_555 A U 9 1_555 B A 14 1_555 -0.591 -0.976 3.174 2.932 5.409 38.455 -2.084 1.222 2.963 8.148 -4.416 38.925 5 AA_C9U10:A38A39_BB A 9 ? B 39 ? A 10 ? B 38 ? 1 A U 9 1_555 B A 14 1_555 A C 10 1_555 B G 13 1_555 0.468 -1.911 3.326 -2.178 5.864 26.861 -5.372 -1.487 2.807 12.411 4.610 27.566 6 AA_U10C11:G37A38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A C 10 1_555 B G 13 1_555 A C 11 1_555 B G 12 1_555 -0.578 -1.699 3.257 1.117 6.356 38.026 -3.322 1.008 2.929 9.670 -1.699 38.549 7 AA_C11C12:G36G37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 11 1_555 B G 12 1_555 A G 12 1_555 B C 11 1_555 -0.155 -1.776 3.380 3.032 10.001 26.350 -5.796 0.973 2.517 20.922 -6.344 28.313 8 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 12 1_555 B C 11 1_555 A G 13 1_555 B C 10 1_555 0.422 -1.738 3.120 -0.877 7.992 30.021 -4.604 -0.937 2.570 15.091 1.657 31.055 9 AA_G13G14:C34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A G 13 1_555 B C 10 1_555 A A 14 1_555 B U 9 1_555 -0.099 -1.405 3.209 1.973 7.155 38.441 -2.908 0.371 2.903 10.745 -2.963 39.124 10 AA_G14A15:U33C34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A A 14 1_555 B U 9 1_555 A A 15 1_555 B C 8 1_555 0.188 -1.397 3.400 2.257 10.859 34.928 -3.690 0.006 2.860 17.553 -3.649 36.594 11 AA_A15A16:C32U33_BB A 15 ? B 33 ? A 16 ? B 32 ? 1 A G 18 1_555 B C 6 1_555 A U 19 1_555 B U 5 1_555 -0.776 -1.832 3.563 -0.823 2.681 38.875 -3.094 1.057 3.449 4.022 1.234 38.972 12 AA_G19U20:U29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 19 1_555 B U 5 1_555 A C 20 1_555 B G 4 1_555 0.765 -1.960 2.880 0.487 0.451 26.020 -4.461 -1.581 2.860 1.000 -1.081 26.028 13 AA_U20C21:G28U29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A C 20 1_555 B G 4 1_555 A G 21 1_555 B C 3 1_555 -0.820 -1.618 3.402 1.887 5.110 31.791 -3.818 1.810 3.059 9.244 -3.414 32.242 14 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 21 1_555 B C 3 1_555 A C 22 1_555 B G 2 1_555 0.830 -1.698 3.092 0.756 -0.187 33.305 -2.932 -1.328 3.119 -0.327 -1.319 33.314 15 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? 1 C G 2 1_555 D C 22 1_555 C C 3 1_555 D G 21 1_555 -0.601 -1.802 3.227 0.246 -1.082 38.043 -2.627 0.952 3.271 -1.659 -0.377 38.059 16 CC_G49C50:G91C92_DD C 49 ? D 92 ? C 50 ? D 91 ? 1 C C 3 1_555 D G 21 1_555 C G 4 1_555 D C 20 1_555 0.108 -2.047 3.322 -0.123 6.951 28.417 -5.475 -0.240 2.753 13.897 0.246 29.238 17 CC_C50G51:C90G91_DD C 50 ? D 91 ? C 51 ? D 90 ? 1 C G 4 1_555 D C 20 1_555 C U 5 1_555 D U 19 1_555 -0.351 -1.743 3.075 0.663 4.661 25.410 -5.055 0.950 2.707 10.480 -1.492 25.836 18 CC_G51U52:U89C90_DD C 51 ? D 90 ? C 52 ? D 89 ? 1 C U 5 1_555 D U 19 1_555 C C 6 1_555 D G 18 1_555 1.009 -2.109 3.441 -2.103 3.044 43.407 -3.143 -1.567 3.243 4.106 2.838 43.557 19 CC_U52C53:G88U89_DD C 52 ? D 89 ? C 53 ? D 88 ? 1 C C 8 1_555 D A 15 1_555 C U 9 1_555 D A 14 1_555 -0.261 -0.617 3.418 -3.855 7.795 44.732 -1.506 -0.013 3.282 10.129 5.009 45.527 20 CC_C55U56:A84A85_DD C 55 ? D 85 ? C 56 ? D 84 ? 1 C U 9 1_555 D A 14 1_555 C C 10 1_555 D G 13 1_555 0.906 -2.038 3.157 1.603 6.752 31.708 -4.726 -1.366 2.718 12.175 -2.891 32.439 21 CC_U56C57:G83A84_DD C 56 ? D 84 ? C 57 ? D 83 ? 1 C C 10 1_555 D G 13 1_555 C C 11 1_555 D G 12 1_555 -1.159 -1.950 3.296 0.896 4.101 26.150 -5.296 2.758 2.920 8.989 -1.964 26.479 22 CC_C57C58:G82G83_DD C 57 ? D 83 ? C 58 ? D 82 ? 1 C C 11 1_555 D G 12 1_555 C G 12 1_555 D C 11 1_555 0.142 -1.550 3.113 0.089 9.790 29.236 -4.596 -0.252 2.477 18.745 -0.170 30.798 23 CC_C58G59:C81G82_DD C 58 ? D 82 ? C 59 ? D 81 ? 1 C G 12 1_555 D C 11 1_555 C G 13 1_555 D C 10 1_555 0.646 -1.507 3.184 -1.234 4.370 31.600 -3.485 -1.385 2.928 7.974 2.251 31.916 24 CC_G59G60:C80C81_DD C 59 ? D 81 ? C 60 ? D 80 ? 1 C G 13 1_555 D C 10 1_555 C A 14 1_555 D U 9 1_555 -0.179 -1.614 3.259 5.133 6.182 33.175 -3.683 1.078 2.862 10.634 -8.830 34.107 25 CC_G60A61:U79C80_DD C 60 ? D 80 ? C 61 ? D 79 ? 1 C A 14 1_555 D U 9 1_555 C A 15 1_555 D C 8 1_555 0.814 -1.099 3.058 -2.393 8.141 36.690 -2.649 -1.540 2.705 12.724 3.741 37.626 26 CC_A61A62:C78U79_DD C 61 ? D 79 ? C 62 ? D 78 ? 1 C G 18 1_555 D C 6 1_555 C U 19 1_555 D U 5 1_555 -1.024 -2.267 3.759 1.754 0.899 46.230 -2.971 1.473 3.677 1.144 -2.233 46.269 27 CC_G65U66:U75C76_DD C 65 ? D 76 ? C 66 ? D 75 ? 1 C U 19 1_555 D U 5 1_555 C C 20 1_555 D G 4 1_555 0.874 -1.780 3.079 2.714 1.894 23.152 -4.994 -1.294 3.006 4.689 -6.719 23.384 28 CC_U66C67:G74U75_DD C 66 ? D 75 ? C 67 ? D 74 ? 1 C C 20 1_555 D G 4 1_555 C G 21 1_555 D C 3 1_555 0.492 -1.726 3.338 2.794 11.664 25.112 -6.165 -0.409 2.357 25.081 -6.009 27.788 29 CC_C67G68:C73G74_DD C 67 ? D 74 ? C 68 ? D 73 ? 1 C G 21 1_555 D C 3 1_555 C C 22 1_555 D G 2 1_555 0.538 -1.883 3.169 -2.688 1.556 31.836 -3.685 -1.437 3.021 2.829 4.886 31.984 30 CC_G68C69:G72C73_DD C 68 ? D 73 ? C 69 ? D 72 ? # _atom_sites.entry_id 5XZ1 _atom_sites.fract_transf_matrix[1][1] 0.021097 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.002062 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.030743 _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] 0.010414 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P # loop_