data_8YDC # _entry.id 8YDC # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 8YDC pdb_00008ydc 10.2210/pdb8ydc/pdb WWPDB D_1300045423 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2024-08-21 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8YDC _pdbx_database_status.recvd_initial_deposition_date 2024-02-20 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email yvliu@nankai.edu.cn _pdbx_contact_author.name_first YIJIN _pdbx_contact_author.name_last LIU _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-3643-8683 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Liu, Y.' 1 0000-0002-3643-8683 'Zhan, X.' 2 0000-0001-6651-538X # _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 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 15 _citation.language ? _citation.page_first 6628 _citation.page_last 6628 _citation.title 'The structure and catalytic mechanism of a pseudoknot-containing hammerhead ribozyme.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-024-50892-y _citation.pdbx_database_id_PubMed 39103372 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhan, X.' 1 ? primary 'Wilson, T.J.' 2 0000-0002-3427-593X primary 'Li, Z.' 3 ? primary 'Zhang, J.' 4 ? primary 'Yang, Y.' 5 ? primary 'Lilley, D.M.J.' 6 0000-0001-6882-2818 primary 'Liu, Y.' 7 ? # 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 man 'ribozyme strand' 18715.248 1 ? ? ? ? 2 polymer man ;DNA/RNA (5'-R(*AP*CP*AP*UP*GP*UP*CP*U)-D(P*C)-R(P*UP*GP*GP*GP*A)-3') ; 4447.691 1 ? ? ? ? 3 non-polymer syn "GUANOSINE-5'-TRIPHOSPHATE" 523.180 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no CGAGACAACCAGGAGUCUAUAAAAUUCCCACUGAUGAGACUGGACGAAAGACAUGUAU CGAGACAACCAGGAGUCUAUAAAAUUCCCACUGAUGAGACUGGACGAAAGACAUGUAU A ? 2 'polydeoxyribonucleotide/polyribonucleotide hybrid' no no 'ACAUGUCU(DC)UGGGA' ACAUGUCUCUGGGA B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name "GUANOSINE-5'-TRIPHOSPHATE" _pdbx_entity_nonpoly.comp_id GTP # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 A n 1 4 G n 1 5 A n 1 6 C n 1 7 A n 1 8 A n 1 9 C n 1 10 C n 1 11 A n 1 12 G n 1 13 G n 1 14 A n 1 15 G n 1 16 U n 1 17 C n 1 18 U n 1 19 A n 1 20 U n 1 21 A n 1 22 A n 1 23 A n 1 24 A n 1 25 U n 1 26 U n 1 27 C n 1 28 C n 1 29 C n 1 30 A n 1 31 C n 1 32 U n 1 33 G n 1 34 A n 1 35 U n 1 36 G n 1 37 A n 1 38 G n 1 39 A n 1 40 C n 1 41 U n 1 42 G n 1 43 G n 1 44 A n 1 45 C n 1 46 G n 1 47 A n 1 48 A n 1 49 A n 1 50 G n 1 51 A n 1 52 C n 1 53 A n 1 54 U n 1 55 G n 1 56 U n 1 57 A n 1 58 U n 2 1 A n 2 2 C n 2 3 A n 2 4 U n 2 5 G n 2 6 U n 2 7 C n 2 8 U n 2 9 DC n 2 10 U n 2 11 G n 2 12 G n 2 13 G n 2 14 A n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample 'Biological sequence' 1 58 ? ? ? ? ? ? ? ? ? 'synthetic construct' 32630 ? ? ? ? ? ? ? ? 'synthetic construct (code 3)' 2577081 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 'Biological sequence' 1 14 ? ? ? ? ? ? ? ? ? 'synthetic construct' 32630 ? ? ? ? ? ? ? ? 'synthetic construct' 32630 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 -1 -1 C C A . n A 1 2 G 2 0 0 G G A . n A 1 3 A 3 1 1 A A A . n A 1 4 G 4 2 2 G G A . n A 1 5 A 5 3 3 A A A . n A 1 6 C 6 4 4 C C A . n A 1 7 A 7 5 5 A A A . n A 1 8 A 8 6 6 A A A . n A 1 9 C 9 7 7 C C A . n A 1 10 C 10 8 8 C C A . n A 1 11 A 11 9 9 A A A . n A 1 12 G 12 10 10 G G A . n A 1 13 G 13 11 11 G G A . n A 1 14 A 14 12 12 A A A . n A 1 15 G 15 13 13 G G A . n A 1 16 U 16 14 14 U U A . n A 1 17 C 17 15 15 C C A . n A 1 18 U 18 16 16 U U A . n A 1 19 A 19 17 17 A A A . n A 1 20 U 20 18 18 U U A . n A 1 21 A 21 19 19 A A A . n A 1 22 A 22 20 20 A A A . n A 1 23 A 23 21 21 A A A . n A 1 24 A 24 22 22 A A A . n A 1 25 U 25 23 23 U U A . n A 1 26 U 26 24 24 U U A . n A 1 27 C 27 25 25 C C A . n A 1 28 C 28 26 26 C C A . n A 1 29 C 29 27 27 C C A . n A 1 30 A 30 28 28 A A A . n A 1 31 C 31 29 29 C C A . n A 1 32 U 32 30 30 U U A . n A 1 33 G 33 31 31 G G A . n A 1 34 A 34 32 32 A A A . n A 1 35 U 35 33 33 U U A . n A 1 36 G 36 34 34 G G A . n A 1 37 A 37 35 35 A A A . n A 1 38 G 38 36 36 G G A . n A 1 39 A 39 37 37 A A A . n A 1 40 C 40 38 38 C C A . n A 1 41 U 41 39 39 U U A . n A 1 42 G 42 40 40 G G A . n A 1 43 G 43 41 41 G G A . n A 1 44 A 44 42 42 A A A . n A 1 45 C 45 43 43 C C A . n A 1 46 G 46 44 44 G G A . n A 1 47 A 47 45 45 A A A . n A 1 48 A 48 46 46 A A A . n A 1 49 A 49 47 47 A A A . n A 1 50 G 50 48 48 G G A . n A 1 51 A 51 49 49 A A A . n A 1 52 C 52 50 50 C C A . n A 1 53 A 53 51 51 A A A . n A 1 54 U 54 52 52 U U A . n A 1 55 G 55 53 53 G G A . n A 1 56 U 56 54 54 U U A . n A 1 57 A 57 55 55 A A A . n A 1 58 U 58 56 ? ? ? A . n B 2 1 A 1 1 1 A A B . n B 2 2 C 2 2 2 C C B . n B 2 3 A 3 3 3 A A B . n B 2 4 U 4 4 4 U U B . n B 2 5 G 5 5 5 G G B . n B 2 6 U 6 6 6 U U B . n B 2 7 C 7 7 7 C C B . n B 2 8 U 8 8 8 U U B . n B 2 9 DC 9 9 9 DC DC B . n B 2 10 U 10 10 10 U U B . n B 2 11 G 11 11 11 G G B . n B 2 12 G 12 12 12 G G B . n B 2 13 G 13 13 13 G G B . n B 2 14 A 14 14 14 A A B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id GTP _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num -2 _pdbx_nonpoly_scheme.pdb_mon_id GTP _pdbx_nonpoly_scheme.auth_mon_id GTP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # 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 ? ? ? '(1.20.1_4487: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? DIALS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? DIALS ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 8YDC _cell.details ? _cell.formula_units_Z ? _cell.length_a 83.578 _cell.length_a_esd ? _cell.length_b 83.578 _cell.length_b_esd ? _cell.length_c 258.790 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _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 8YDC _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8YDC _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 5.51 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 77.69 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;Magnesium acetate tetrahydrate MES monohydrate Ammonium sulfate ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 277 # _diffrn.ambient_environment ? _diffrn.ambient_temp 93 _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 EIGER2 S 9M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2021-07-04 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.979183 _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 'SSRF BEAMLINE BL02U1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.979183 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL02U1 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 8YDC _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.89 _reflns.d_resolution_low 16.25 _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 12665 _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 98.38 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 37.8 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 18.05 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _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 ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 2.89 _reflns_shell.d_res_low 2.993 _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 1226 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.866 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _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 ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8YDC _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 2.89 _refine.ls_d_res_low 16.25 _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 12565 _refine.ls_number_reflns_R_free 642 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.20 _refine.ls_percent_reflns_R_free 5.11 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1960 _refine.ls_R_factor_R_free 0.2091 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1954 _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 1.34 _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 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 27.57 _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 0.42 _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 LAST _refine_hist.details ? _refine_hist.d_res_high 2.89 _refine_hist.d_res_low 16.25 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1549 _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 ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1549 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.009 ? ? ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.866 ? ? ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 16.742 ? 857 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.076 ? 356 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.011 ? 72 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 2.89 3.11 . . 117 2304 99.00 . . . . 0.3742 . . . . . . . . . . . 0.4001 'X-RAY DIFFRACTION' 3.11 3.42 . . 142 2295 99.00 . . . . 0.2458 . . . . . . . . . . . 0.2923 'X-RAY DIFFRACTION' 3.42 3.91 . . 131 2343 99.00 . . . . 0.2282 . . . . . . . . . . . 0.2551 'X-RAY DIFFRACTION' 3.91 4.91 . . 123 2407 99.00 . . . . . . . . . . . . . . . . 0.1591 # _struct.entry_id 8YDC _struct.title 'Crystal structure of a hammerhead ribozyme with pseudoknot' _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 8YDC _struct_keywords.text 'catalysis, 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 2 ? C N N 3 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 8YDC 8YDC ? 1 ? 1 2 PDB 8YDC 8YDC ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 8YDC A 1 ? 58 ? 8YDC -1 ? 56 ? -1 56 2 2 8YDC B 1 ? 14 ? 8YDC 1 ? 14 ? 1 14 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _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] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A C 1 P ? ? ? 1_555 C GTP . "O3'" ? ? A C -1 A GTP 101 1_555 ? ? ? ? ? ? ? 1.559 ? ? hydrog1 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 18 N3 ? ? A A 1 A U 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 18 O4 ? ? A A 1 A U 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 4 N2 ? ? ? 1_555 A U 20 O4 ? ? A G 2 A U 18 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog7 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 16 N3 ? ? A A 3 A U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 16 O4 ? ? A A 3 A U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 4 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 4 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 4 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 O2 ? ? ? 1_555 A A 22 N6 ? ? A C 4 A A 20 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog13 hydrog ? ? A C 6 O2 ? ? ? 1_555 A A 23 N6 ? ? A C 4 A A 21 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog14 hydrog ? ? A A 7 N1 ? ? ? 1_555 A A 14 N6 ? ? A A 5 A A 12 1_555 ? ? ? ? ? ? TYPE_1_PAIR ? ? ? hydrog15 hydrog ? ? A A 7 N6 ? ? ? 1_555 A A 14 N1 ? ? A A 5 A A 12 1_555 ? ? ? ? ? ? TYPE_1_PAIR ? ? ? hydrog16 hydrog ? ? A A 7 N6 ? ? ? 1_555 A A 24 N1 ? ? A A 5 A A 22 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog17 hydrog ? ? A A 7 N7 ? ? ? 1_555 A A 24 N6 ? ? A A 5 A A 22 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 A A 44 N1 ? ? A A 6 A A 42 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog19 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 43 N1 ? ? A C 7 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 43 O6 ? ? A C 7 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 43 N2 ? ? A C 7 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 42 N1 ? ? A C 8 A G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 42 O6 ? ? A C 8 A G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 42 N2 ? ? A C 8 A G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A A 11 N1 ? ? ? 1_555 A U 41 N3 ? ? A A 9 A U 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 11 N6 ? ? ? 1_555 A U 41 O4 ? ? A A 9 A U 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 40 N3 ? ? A G 10 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 40 O2 ? ? A G 10 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 40 N4 ? ? A G 10 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 13 N2 ? ? ? 1_555 A U 25 O2 ? ? A G 11 A U 23 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog31 hydrog ? ? A G 13 N1 ? ? ? 1_555 A A 39 N1 ? ? A G 11 A A 37 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog32 hydrog ? ? A G 13 O6 ? ? ? 1_555 A A 39 N6 ? ? A G 11 A A 37 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog33 hydrog ? ? A G 15 N2 ? ? ? 1_555 A A 23 N1 ? ? A G 13 A A 21 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog34 hydrog ? ? A U 16 O2 ? ? ? 1_555 A A 22 N6 ? ? A U 14 A A 20 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog35 hydrog ? ? A C 17 O2 ? ? ? 1_555 A A 21 N6 ? ? A C 15 A A 19 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog36 hydrog ? ? A U 25 N3 ? ? ? 1_555 A A 39 N3 ? ? A U 23 A A 37 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog37 hydrog ? ? A U 26 N3 ? ? ? 1_555 B A 14 N1 ? ? A U 24 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 26 O4 ? ? ? 1_555 B A 14 N6 ? ? A U 24 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 27 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 25 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 27 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 25 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 27 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 25 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 28 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 26 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 28 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 26 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 28 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 26 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 29 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 27 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 29 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 27 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 29 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 27 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A A 30 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 28 B U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A A 30 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 28 B U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 31 N3 ? ? ? 1_555 A G 36 N1 ? ? A C 29 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 31 N4 ? ? ? 1_555 A G 36 O6 ? ? A C 29 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 31 O2 ? ? ? 1_555 A G 36 N2 ? ? A C 29 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A G 33 N2 ? ? ? 1_555 A A 48 N1 ? ? A G 31 A A 46 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog54 hydrog ? ? A A 37 N6 ? ? ? 1_555 A G 46 N3 ? ? A A 35 A G 44 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog55 hydrog ? ? A A 37 N7 ? ? ? 1_555 A G 46 N2 ? ? A A 35 A G 44 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog56 hydrog ? ? A G 38 N1 ? ? ? 1_555 A C 45 N3 ? ? A G 36 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A G 38 N2 ? ? ? 1_555 A C 45 O2 ? ? A G 36 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A G 38 O6 ? ? ? 1_555 A C 45 N4 ? ? A G 36 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A A 49 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 47 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A A 49 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 47 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A G 50 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 48 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A G 50 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 48 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A G 50 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 48 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A A 51 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 49 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A A 51 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 49 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 52 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 50 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 52 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 50 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 52 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 50 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A A 53 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 51 B U 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A A 53 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 51 B U 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A U 54 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 52 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A U 54 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 52 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A G 55 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 53 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A G 55 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 53 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A G 55 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 53 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A U 56 N3 ? ? ? 1_555 B A 1 N1 ? ? A U 54 B A 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? A U 56 O4 ? ? ? 1_555 B A 1 N6 ? ? A U 54 B A 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "C5'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 G _pdbx_validate_rmsd_bond.auth_seq_id_1 36 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C4'" _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 36 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.466 _pdbx_validate_rmsd_bond.bond_target_value 1.508 _pdbx_validate_rmsd_bond.bond_deviation -0.042 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.007 _pdbx_validate_rmsd_bond.linker_flag N # 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 "O5'" A A 6 ? ? P A A 6 ? ? OP1 A A 6 ? ? 117.93 110.70 7.23 1.20 N 2 1 "O3'" A A 6 ? ? P A C 7 ? ? OP2 A C 7 ? ? 117.12 110.50 6.62 1.10 Y 3 1 C6 A C 7 ? ? N1 A C 7 ? ? C2 A C 7 ? ? 117.78 120.30 -2.52 0.40 N 4 1 C5 A U 18 ? ? C6 A U 18 ? ? N1 A U 18 ? ? 118.32 122.70 -4.38 0.50 N 5 1 N3 A U 18 ? ? C4 A U 18 ? ? O4 A U 18 ? ? 114.90 119.40 -4.50 0.70 N 6 1 C5 A U 18 ? ? C4 A U 18 ? ? O4 A U 18 ? ? 129.86 125.90 3.96 0.60 N 7 1 C2 A U 18 ? ? N1 A U 18 ? ? "C1'" A U 18 ? ? 109.12 117.70 -8.58 1.20 N 8 1 "O4'" A A 19 ? ? "C1'" A A 19 ? ? N9 A A 19 ? ? 112.71 108.50 4.21 0.70 N 9 1 "O4'" A G 36 ? ? "C1'" A G 36 ? ? N9 A G 36 ? ? 113.88 108.50 5.38 0.70 N 10 1 "O3'" A A 37 ? ? P A C 38 ? ? OP2 A C 38 ? ? 118.49 110.50 7.99 1.10 Y 11 1 "O3'" A A 37 ? ? P A C 38 ? ? OP1 A C 38 ? ? 90.77 105.20 -14.43 2.20 Y 12 1 C6 A C 38 ? ? N1 A C 38 ? ? C2 A C 38 ? ? 122.94 120.30 2.64 0.40 N 13 1 "O3'" B U 8 ? ? P B DC 9 ? ? OP2 B DC 9 ? ? 119.15 110.50 8.65 1.10 Y 14 1 OP1 B DC 9 ? ? P B DC 9 ? ? OP2 B DC 9 ? ? 106.07 119.60 -13.53 1.50 N # _pdbx_entry_details.entry_id 8YDC _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification ? # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id U _pdbx_unobs_or_zero_occ_residues.auth_seq_id 56 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id U _pdbx_unobs_or_zero_occ_residues.label_seq_id 58 # 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 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 GTP PG P N N 145 GTP O1G O N N 146 GTP O2G O N N 147 GTP O3G O N N 148 GTP O3B O N N 149 GTP PB P N N 150 GTP O1B O N N 151 GTP O2B O N N 152 GTP O3A O N N 153 GTP PA P N N 154 GTP O1A O N N 155 GTP O2A O N N 156 GTP "O5'" O N N 157 GTP "C5'" C N N 158 GTP "C4'" C N R 159 GTP "O4'" O N N 160 GTP "C3'" C N S 161 GTP "O3'" O N N 162 GTP "C2'" C N R 163 GTP "O2'" O N N 164 GTP "C1'" C N R 165 GTP N9 N Y N 166 GTP C8 C Y N 167 GTP N7 N Y N 168 GTP C5 C Y N 169 GTP C6 C N N 170 GTP O6 O N N 171 GTP N1 N N N 172 GTP C2 C N N 173 GTP N2 N N N 174 GTP N3 N N N 175 GTP C4 C Y N 176 GTP HOG2 H N N 177 GTP HOG3 H N N 178 GTP HOB2 H N N 179 GTP HOA2 H N N 180 GTP "H5'" H N N 181 GTP "H5''" H N N 182 GTP "H4'" H N N 183 GTP "H3'" H N N 184 GTP "HO3'" H N N 185 GTP "H2'" H N N 186 GTP "HO2'" H N N 187 GTP "H1'" H N N 188 GTP H8 H N N 189 GTP HN1 H N N 190 GTP HN21 H N N 191 GTP HN22 H N N 192 U OP3 O N N 193 U P P N N 194 U OP1 O N N 195 U OP2 O N N 196 U "O5'" O N N 197 U "C5'" C N N 198 U "C4'" C N R 199 U "O4'" O N N 200 U "C3'" C N S 201 U "O3'" O N N 202 U "C2'" C N R 203 U "O2'" O N N 204 U "C1'" C N R 205 U N1 N N N 206 U C2 C N N 207 U O2 O N N 208 U N3 N N N 209 U C4 C N N 210 U O4 O N N 211 U C5 C N N 212 U C6 C N N 213 U HOP3 H N N 214 U HOP2 H N N 215 U "H5'" H N N 216 U "H5''" H N N 217 U "H4'" H N N 218 U "H3'" H N N 219 U "HO3'" H N N 220 U "H2'" H N N 221 U "HO2'" H N N 222 U "H1'" H N N 223 U H3 H N N 224 U H5 H N N 225 U H6 H N N 226 # 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 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 GTP PG O1G doub N N 151 GTP PG O2G sing N N 152 GTP PG O3G sing N N 153 GTP PG O3B sing N N 154 GTP O2G HOG2 sing N N 155 GTP O3G HOG3 sing N N 156 GTP O3B PB sing N N 157 GTP PB O1B doub N N 158 GTP PB O2B sing N N 159 GTP PB O3A sing N N 160 GTP O2B HOB2 sing N N 161 GTP O3A PA sing N N 162 GTP PA O1A doub N N 163 GTP PA O2A sing N N 164 GTP PA "O5'" sing N N 165 GTP O2A HOA2 sing N N 166 GTP "O5'" "C5'" sing N N 167 GTP "C5'" "C4'" sing N N 168 GTP "C5'" "H5'" sing N N 169 GTP "C5'" "H5''" sing N N 170 GTP "C4'" "O4'" sing N N 171 GTP "C4'" "C3'" sing N N 172 GTP "C4'" "H4'" sing N N 173 GTP "O4'" "C1'" sing N N 174 GTP "C3'" "O3'" sing N N 175 GTP "C3'" "C2'" sing N N 176 GTP "C3'" "H3'" sing N N 177 GTP "O3'" "HO3'" sing N N 178 GTP "C2'" "O2'" sing N N 179 GTP "C2'" "C1'" sing N N 180 GTP "C2'" "H2'" sing N N 181 GTP "O2'" "HO2'" sing N N 182 GTP "C1'" N9 sing N N 183 GTP "C1'" "H1'" sing N N 184 GTP N9 C8 sing Y N 185 GTP N9 C4 sing Y N 186 GTP C8 N7 doub Y N 187 GTP C8 H8 sing N N 188 GTP N7 C5 sing Y N 189 GTP C5 C6 sing N N 190 GTP C5 C4 doub Y N 191 GTP C6 O6 doub N N 192 GTP C6 N1 sing N N 193 GTP N1 C2 sing N N 194 GTP N1 HN1 sing N N 195 GTP C2 N2 sing N N 196 GTP C2 N3 doub N N 197 GTP N2 HN21 sing N N 198 GTP N2 HN22 sing N N 199 GTP N3 C4 sing N N 200 U OP3 P sing N N 201 U OP3 HOP3 sing N N 202 U P OP1 doub N N 203 U P OP2 sing N N 204 U P "O5'" sing N N 205 U OP2 HOP2 sing N N 206 U "O5'" "C5'" sing N N 207 U "C5'" "C4'" sing N N 208 U "C5'" "H5'" sing N N 209 U "C5'" "H5''" sing N N 210 U "C4'" "O4'" sing N N 211 U "C4'" "C3'" sing N N 212 U "C4'" "H4'" sing N N 213 U "O4'" "C1'" sing N N 214 U "C3'" "O3'" sing N N 215 U "C3'" "C2'" sing N N 216 U "C3'" "H3'" sing N N 217 U "O3'" "HO3'" sing N N 218 U "C2'" "O2'" sing N N 219 U "C2'" "C1'" sing N N 220 U "C2'" "H2'" sing N N 221 U "O2'" "HO2'" sing N N 222 U "C1'" N1 sing N N 223 U "C1'" "H1'" sing N N 224 U N1 C2 sing N N 225 U N1 C6 sing N N 226 U C2 O2 doub N N 227 U C2 N3 sing N N 228 U N3 C4 sing N N 229 U N3 H3 sing N N 230 U C4 O4 doub N N 231 U C4 C5 sing N N 232 U C5 C6 doub N N 233 U C5 H5 sing N N 234 U C6 H6 sing N N 235 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8YDC 'double helix' 8YDC 'a-form double helix' 8YDC 'mismatched base pair' 8YDC 'quadruple 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 A 3 1_555 A U 18 1_555 0.196 -0.082 0.038 -7.316 -5.222 -2.699 1 A_A1:U16_A A 1 ? A 16 ? 20 1 1 A G 4 1_555 A C 17 1_555 -0.076 -0.114 0.012 -5.183 -14.574 1.875 2 A_G2:C15_A A 2 ? A 15 ? 19 1 1 A A 5 1_555 A U 16 1_555 0.314 -0.189 0.593 6.905 -13.349 8.293 3 A_A3:U14_A A 3 ? A 14 ? 20 1 1 A C 6 1_555 A G 15 1_555 0.404 -0.166 0.246 7.709 -9.525 -1.411 4 A_C4:G13_A A 4 ? A 13 ? 19 1 1 A A 7 1_555 A A 14 1_555 1.717 1.740 0.056 -8.963 16.201 -176.071 5 A_A5:A12_A A 5 ? A 12 ? 1 2 1 A A 39 1_555 A G 13 1_555 -0.140 1.522 0.260 28.553 -16.650 -30.469 6 A_A37:G11_A A 37 ? A 11 ? 8 1 1 A C 40 1_555 A G 12 1_555 0.277 -0.265 0.413 15.586 -25.228 -8.306 7 A_C38:G10_A A 38 ? A 10 ? 19 1 1 A U 41 1_555 A A 11 1_555 -0.330 -0.068 0.121 12.098 -18.538 2.565 8 A_U39:A9_A A 39 ? A 9 ? 20 1 1 A G 42 1_555 A C 10 1_555 -0.621 -0.192 0.113 -1.965 -12.073 1.623 9 A_G40:C8_A A 40 ? A 8 ? 19 1 1 A G 43 1_555 A C 9 1_555 -0.246 0.007 0.394 -15.221 -23.395 3.827 10 A_G41:C7_A A 41 ? A 7 ? 19 1 1 A A 44 1_555 A A 8 1_555 1.791 1.757 0.493 -26.621 -11.953 -9.785 11 A_A42:A6_A A 42 ? A 6 ? ? 1 1 A C 45 1_555 A G 38 1_555 0.434 0.065 0.167 -26.167 24.432 5.344 12 A_C43:G36_A A 43 ? A 36 ? 19 1 1 A G 46 1_555 A A 37 1_555 6.217 -3.986 1.462 13.475 15.053 14.369 13 A_G44:A35_A A 44 ? A 35 ? 11 9 1 A U 26 1_555 B A 14 1_555 -0.007 0.138 -0.423 7.915 -18.740 1.100 14 A_U24:A14_B A 24 ? B 14 ? 20 1 1 A C 27 1_555 B G 13 1_555 0.578 0.091 0.287 8.484 -17.288 5.876 15 A_C25:G13_B A 25 ? B 13 ? 19 1 1 A C 28 1_555 B G 12 1_555 0.304 -0.035 -0.344 16.215 -13.464 3.437 16 A_C26:G12_B A 26 ? B 12 ? 19 1 1 A C 29 1_555 B G 11 1_555 0.652 -0.213 -0.246 6.312 -15.675 0.598 17 A_C27:G11_B A 27 ? B 11 ? 19 1 1 A A 30 1_555 B U 10 1_555 0.798 -0.064 0.679 8.967 -10.255 -2.185 18 A_A28:U10_B A 28 ? B 10 ? 20 1 1 A C 31 1_555 A G 36 1_555 0.787 0.043 0.115 13.522 -2.399 -0.359 19 A_C29:G34_A A 29 ? A 34 ? 19 1 1 A A 48 1_555 A G 33 1_555 -3.791 3.538 0.620 41.748 -40.936 84.060 20 A_A46:G31_A A 46 ? A 31 ? ? ? 1 A A 49 1_555 B U 8 1_555 0.266 -0.106 0.490 -1.686 -6.458 -3.884 21 A_A47:U8_B A 47 ? B 8 ? 20 1 1 A G 50 1_555 B C 7 1_555 0.282 0.224 0.121 3.547 -13.400 1.292 22 A_G48:C7_B A 48 ? B 7 ? 19 1 1 A A 51 1_555 B U 6 1_555 0.283 0.012 -0.109 1.939 -14.965 -0.459 23 A_A49:U6_B A 49 ? B 6 ? 20 1 1 A C 52 1_555 B G 5 1_555 0.484 -0.110 -0.129 1.847 -12.352 5.321 24 A_C50:G5_B A 50 ? B 5 ? 19 1 1 A A 53 1_555 B U 4 1_555 -0.093 -0.051 0.851 2.872 -0.989 3.650 25 A_A51:U4_B A 51 ? B 4 ? 20 1 1 A U 54 1_555 B A 3 1_555 0.099 -0.001 0.377 -2.237 -11.663 6.234 26 A_U52:A3_B A 52 ? B 3 ? 20 1 1 A G 55 1_555 B C 2 1_555 -0.592 0.090 0.046 -9.799 -20.757 5.808 27 A_G53:C2_B A 53 ? B 2 ? 19 1 1 A U 56 1_555 B A 1 1_555 0.057 -0.152 0.413 -9.507 -11.690 -2.368 28 A_U54:A1_B A 54 ? B 1 ? 20 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 A 3 1_555 A U 18 1_555 A G 4 1_555 A C 17 1_555 0.553 -1.497 3.168 1.796 11.587 29.653 -4.615 -0.715 2.453 21.606 -3.350 31.839 1 AA_A1G2:C15U16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A G 4 1_555 A C 17 1_555 A A 5 1_555 A U 16 1_555 0.260 -0.778 2.851 -2.707 -1.701 36.602 -1.032 -0.735 2.857 -2.702 4.300 36.737 2 AA_G2A3:U14C15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A A 5 1_555 A U 16 1_555 A C 6 1_555 A G 15 1_555 0.081 -1.218 3.264 4.533 1.919 34.159 -2.347 0.559 3.177 3.246 -7.667 34.502 3 AA_A3C4:G13U14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A C 6 1_555 A G 15 1_555 A A 7 1_555 A A 14 1_555 3.504 -0.665 -0.922 -100.967 -146.231 -154.266 0.263 1.800 -0.577 73.139 -50.500 -179.488 4 AA_C4A5:A12G13_AA A 4 ? A 13 ? A 5 ? A 12 ? 1 A A 7 1_555 A A 14 1_555 A A 39 1_555 A G 13 1_555 3.161 -0.988 -0.315 123.282 124.346 177.487 -0.492 -1.583 -0.282 62.173 -61.641 179.893 5 AA_A5A37:G11A12_AA A 5 ? A 12 ? A 37 ? A 11 ? 1 A A 39 1_555 A G 13 1_555 A C 40 1_555 A G 12 1_555 1.108 -1.800 3.147 -4.051 5.331 43.209 -2.885 -1.844 2.807 7.188 5.461 43.700 6 AA_A37C38:G10G11_AA A 37 ? A 11 ? A 38 ? A 10 ? 1 A C 40 1_555 A G 12 1_555 A U 41 1_555 A A 11 1_555 -0.377 -1.557 3.223 -0.697 10.332 30.836 -4.436 0.562 2.588 18.778 1.266 32.488 7 AA_C38U39:A9G10_AA A 38 ? A 10 ? A 39 ? A 9 ? 1 A U 41 1_555 A A 11 1_555 A G 42 1_555 A C 10 1_555 0.297 -1.438 3.326 -0.666 18.839 33.420 -4.356 -0.530 2.227 29.981 1.061 38.237 8 AA_U39G40:C8A9_AA A 39 ? A 9 ? A 40 ? A 8 ? 1 A G 42 1_555 A C 10 1_555 A G 43 1_555 A C 9 1_555 1.263 -1.809 3.293 5.939 12.187 38.151 -3.928 -1.191 2.770 17.966 -8.756 40.404 9 AA_G40G41:C7C8_AA A 40 ? A 8 ? A 41 ? A 7 ? 1 A G 43 1_555 A C 9 1_555 A A 44 1_555 A A 8 1_555 -0.172 -1.376 3.352 6.648 3.854 41.589 -2.305 0.922 3.155 5.372 -9.268 42.262 10 AA_G41A42:A6C7_AA A 41 ? A 7 ? A 42 ? A 6 ? 1 A A 44 1_555 A A 8 1_555 A C 45 1_555 A G 38 1_555 2.706 -0.102 3.536 3.601 0.567 30.168 -0.323 -4.348 3.823 1.084 -6.888 30.382 11 AA_A42C43:G36A6_AA A 42 ? A 6 ? A 43 ? A 36 ? 1 A C 45 1_555 A G 38 1_555 A G 46 1_555 A A 37 1_555 0.399 1.189 2.349 2.488 20.372 43.527 0.163 -0.333 2.646 25.832 -3.155 47.910 12 AA_C43G44:A35G36_AA A 43 ? A 36 ? A 44 ? A 35 ? 1 A U 26 1_555 B A 14 1_555 A C 27 1_555 B G 13 1_555 -0.687 -1.846 3.269 -9.487 8.603 27.164 -5.260 -0.537 2.661 17.160 18.922 29.980 13 AA_U24C25:G13A14_BB A 24 ? B 14 ? A 25 ? B 13 ? 1 A C 27 1_555 B G 13 1_555 A C 28 1_555 B G 12 1_555 -0.601 -1.799 2.916 1.186 7.435 33.604 -4.004 1.169 2.452 12.663 -2.021 34.413 14 AA_C25C26:G12G13_BB A 25 ? B 13 ? A 26 ? B 12 ? 1 A C 28 1_555 B G 12 1_555 A C 29 1_555 B G 11 1_555 -0.509 -1.363 3.584 0.217 6.529 32.539 -3.545 0.930 3.254 11.508 -0.382 33.171 15 AA_C26C27:G11G12_BB A 26 ? B 12 ? A 27 ? B 11 ? 1 A C 29 1_555 B G 11 1_555 A A 30 1_555 B U 10 1_555 -0.140 -1.356 3.094 -4.621 6.847 35.259 -3.062 -0.367 2.786 11.116 7.502 36.183 16 AA_C27A28:U10G11_BB A 27 ? B 11 ? A 28 ? B 10 ? 1 A A 30 1_555 B U 10 1_555 A C 31 1_555 A G 36 1_555 -0.671 -0.958 3.334 7.632 16.332 22.592 -5.222 2.888 1.912 35.335 -16.512 28.830 17 AA_A28C29:G34U10_AB A 28 ? B 10 ? A 29 ? A 34 ? 1 A A 48 1_555 A G 33 1_555 A A 49 1_555 B U 8 1_555 0.610 2.574 3.706 -1.391 -19.348 87.401 2.264 -0.465 3.197 -13.859 0.996 89.102 18 AA_A46A47:U8G31_BA A 46 ? A 31 ? A 47 ? B 8 ? 1 A A 49 1_555 B U 8 1_555 A G 50 1_555 B C 7 1_555 0.146 -1.122 3.352 1.966 4.342 30.822 -2.916 0.105 3.171 8.108 -3.672 31.179 19 AA_A47G48:C7U8_BB A 47 ? B 8 ? A 48 ? B 7 ? 1 A G 50 1_555 B C 7 1_555 A A 51 1_555 B U 6 1_555 0.166 -1.448 3.276 2.239 7.045 30.333 -3.971 0.097 2.880 13.219 -4.201 31.200 20 AA_G48A49:U6C7_BB A 48 ? B 7 ? A 49 ? B 6 ? 1 A A 51 1_555 B U 6 1_555 A C 52 1_555 B G 5 1_555 1.078 -1.468 3.150 5.919 4.228 35.535 -2.931 -0.932 3.095 6.838 -9.575 36.248 21 AA_A49C50:G5U6_BB A 49 ? B 6 ? A 50 ? B 5 ? 1 A C 52 1_555 B G 5 1_555 A A 53 1_555 B U 4 1_555 -0.541 -2.645 3.161 -5.550 4.698 20.526 -8.669 -0.531 2.555 12.682 14.981 21.762 22 AA_C50A51:U4G5_BB A 50 ? B 5 ? A 51 ? B 4 ? 1 A A 53 1_555 B U 4 1_555 A U 54 1_555 B A 3 1_555 0.226 -1.285 3.344 4.929 12.480 33.574 -3.775 0.307 2.716 20.612 -8.140 36.085 23 AA_A51U52:A3U4_BB A 51 ? B 4 ? A 52 ? B 3 ? 1 A U 54 1_555 B A 3 1_555 A G 55 1_555 B C 2 1_555 -0.073 -1.554 3.261 0.114 10.454 32.888 -4.129 0.139 2.657 17.909 -0.196 34.466 24 AA_U52G53:C2A3_BB A 52 ? B 3 ? A 53 ? B 2 ? 1 A G 55 1_555 B C 2 1_555 A U 56 1_555 B A 1 1_555 -0.460 -0.975 3.275 -4.062 5.143 36.152 -2.243 0.181 3.143 8.205 6.480 36.722 25 AA_G53U54:A1C2_BB A 53 ? B 2 ? A 54 ? B 1 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Science Foundation (NSF, China)' China 82111530210 1 'National Science Foundation (NSF, China)' China 21877065 2 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id GTP _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id GTP _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _atom_sites.entry_id 8YDC _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.011965 _atom_sites.fract_transf_matrix[1][2] 0.006908 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.013816 _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] 0.003864 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O P # loop_