data_1YKV # _entry.id 1YKV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1YKV pdb_00001ykv 10.2210/pdb1ykv/pdb NDB UR0054 ? ? RCSB RCSB031631 ? ? WWPDB D_1000031631 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1YKQ 'The same ribozyme complexed with the reaction product' unspecified PDB 1YLS . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YKV _pdbx_database_status.recvd_initial_deposition_date 2005-01-18 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Serganov, A.' 1 'Keiper, S.' 2 'Malinina, L.' 3 'Tereshko, V.' 4 'Skripkin, E.' 5 'Hobartner, C.' 6 'Polonskaia, A.' 7 'Phan, A.T.' 8 'Wombacher, R.' 9 'Micura, R.' 10 'Dauter, Z.' 11 'Jaschke, A.' 12 'Patel, D.J.' 13 # _citation.id primary _citation.title 'Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 12 _citation.page_first 218 _citation.page_last 224 _citation.year 2005 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9993 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15723077 _citation.pdbx_database_id_DOI 10.1038/nsmb906 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Serganov, A.' 1 ? primary 'Keiper, S.' 2 ? primary 'Malinina, L.' 3 ? primary 'Tereshko, V.' 4 ? primary 'Skripkin, E.' 5 ? primary 'Hobartner, C.' 6 ? primary 'Polonskaia, A.' 7 ? primary 'Phan, A.T.' 8 ? primary 'Wombacher, R.' 9 ? primary 'Micura, R.' 10 ? primary 'Dauter, Z.' 11 ? primary 'Jaschke, A.' 12 ? primary 'Patel, D.J.' 13 ? # _cell.entry_id 1YKV _cell.length_a 78.288 _cell.length_b 44.039 _cell.length_c 79.998 _cell.angle_alpha 90.00 _cell.angle_beta 106.87 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YKV _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? # 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 'Diels-Alder ribozyme' 3497.146 2 ? ? ? 11-mer 2 polymer syn 'Diels-Alder ribozyme' 12262.333 2 ? ? ? 38-mer 3 non-polymer syn "(3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A-TETRAHYDRO-4,9[1',2']-BENZENO-1H-BENZ[F]ISOINDOLE-1,3(2H)-DIONE" 375.460 2 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 7 ? ? ? ? # 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 GGAGCUCGCCC GGAGCUCGCCC A,C ? 2 polyribonucleotide no no GGGCGAGGCCGUGCCAGCUCUUCGGAGCAAUACUCGGC GGGCGAGGCCGUGCCAGCUCUUCGGAGCAAUACUCGGC B,D ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 A n 1 4 G n 1 5 C n 1 6 U n 1 7 C n 1 8 G n 1 9 C n 1 10 C n 1 11 C n 2 1 G n 2 2 G n 2 3 G n 2 4 C n 2 5 G n 2 6 A n 2 7 G n 2 8 G n 2 9 C n 2 10 C n 2 11 G n 2 12 U n 2 13 G n 2 14 C n 2 15 C n 2 16 A n 2 17 G n 2 18 C n 2 19 U n 2 20 C n 2 21 U n 2 22 U n 2 23 C n 2 24 G n 2 25 G n 2 26 A n 2 27 G n 2 28 C n 2 29 A n 2 30 A n 2 31 U n 2 32 A n 2 33 C n 2 34 U n 2 35 C n 2 36 G n 2 37 G n 2 38 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? ;This RNA was chemically synthesized. The sequence was derived from the in vitro selected ribozyme catalysing Diels-Alder reaction between thethered anthracene and biotinylated maleimide ; 2 1 sample ? ? ? ? ? ;This RNA was chemically synthesized. The sequence was derived from the in vitro selected ribozyme catalysing Diels-Alder reaction between thethered anthracene and biotinylated maleimide ; # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1YKV 1YKV ? ? ? 2 2 PDB 1YKV 1YKV ? ? ? # 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 1YKV A 1 ? 11 ? 1YKV 101 ? 111 ? 101 111 2 2 1YKV B 1 ? 38 ? 1YKV 201 ? 238 ? 201 238 3 1 1YKV C 1 ? 11 ? 1YKV 101 ? 111 ? 101 111 4 2 1YKV D 1 ? 38 ? 1YKV 201 ? 238 ? 201 238 # 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 DAI non-polymer . "(3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A-TETRAHYDRO-4,9[1',2']-BENZENO-1H-BENZ[F]ISOINDOLE-1,3(2H)-DIONE" '(11S,12S)-9-HYDROXYMETHYL-11,12-(2-PENTYL-1,3-DIOXO-2-AZAPROPANO)-9,10-DIHYDRO-9,10-ETHANOANTHRACENE' 'C24 H25 N O3' 375.460 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 1YKV _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.99 _exptl_crystal.density_percent_sol 63 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_details 'PEG400, sodium HEPES, magnesium chloride, ethylacetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 PEG400 ? ? ? 1 2 1 'sodium HEPES' ? ? ? 1 3 1 H2O ? ? ? 1 4 2 PEG400 ? ? ? 1 5 2 'sodium HEPES' ? ? ? 1 6 2 'magnesium chloride' ? ? ? 1 7 2 ethylacetate ? ? ? 1 8 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2002-10-03 _diffrn_detector.details 'Si (111) double-crystal monochromator, Bent cylindrical Si-mirror (Rh coating)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si (111) double-crystal monochromator' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _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.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 14-BM-D' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 14-BM-D _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.1 # _reflns.entry_id 1YKV _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 3.3 _reflns.d_resolution_low 20 _reflns.number_all 8607 _reflns.number_obs 8392 _reflns.percent_possible_obs 97.7 _reflns.pdbx_Rmerge_I_obs 0.092 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 14.0 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.9 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 3.3 _reflns_shell.d_res_low 3.42 _reflns_shell.percent_possible_all 88.9 _reflns_shell.Rmerge_I_obs 0.162 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 8.0 _reflns_shell.pdbx_redundancy 4.4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1YKV _refine.ls_number_reflns_obs 7522 _refine.ls_number_reflns_all 7910 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.00 _refine.ls_d_res_high 3.30 _refine.ls_percent_reflns_obs 97.70 _refine.ls_R_factor_obs 0.22971 _refine.ls_R_factor_all 0.22971 _refine.ls_R_factor_R_work 0.22802 _refine.ls_R_factor_R_free 0.26206 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.9 _refine.ls_number_reflns_R_free 388 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.899 _refine.correlation_coeff_Fo_to_Fc_free 0.862 _refine.B_iso_mean 21.884 _refine.aniso_B[1][1] 3.52 _refine.aniso_B[2][2] -3.78 _refine.aniso_B[3][3] -0.22 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] -0.82 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'The Diels-Alder ribozyme structure from the Diels-Alder ribozyme-product complex, pdb entry 1YLS' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 0.474 _refine.overall_SU_ML 0.383 _refine.overall_SU_B 53.158 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1YKV _refine_analyze.Luzzati_coordinate_error_obs 0.607 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 2092 _refine_hist.pdbx_number_atoms_ligand 63 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 2155 _refine_hist.d_res_high 3.30 _refine_hist.d_res_low 20.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.016 0.021 ? 2404 'X-RAY DIFFRACTION' ? r_bond_other_d 0.006 0.020 ? 846 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.480 3.000 ? 3734 'X-RAY DIFFRACTION' ? r_angle_other_deg 2.597 3.000 ? 2200 'X-RAY DIFFRACTION' ? r_chiral_restr 0.094 0.200 ? 496 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 1074 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.009 0.020 ? 16 'X-RAY DIFFRACTION' ? r_nbd_refined 0.168 0.200 ? 593 'X-RAY DIFFRACTION' ? r_nbd_other 0.310 0.200 ? 1154 'X-RAY DIFFRACTION' ? r_nbtor_other 0.115 0.200 ? 589 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.141 0.200 ? 46 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other 0.369 0.200 ? 2 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.206 0.200 ? 40 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.223 0.200 ? 11 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.130 0.200 ? 3 'X-RAY DIFFRACTION' ? r_scbond_it 0.639 3.000 ? 3432 'X-RAY DIFFRACTION' ? r_scangle_it 0.599 4.500 ? 3734 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.pdbx_refine_id _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso _refine_ls_restr_ncs.pdbx_asym_id _refine_ls_restr_ncs.pdbx_rms _refine_ls_restr_ncs.pdbx_weight 1 'loose positional' A 376 0.30 5.00 1 'X-RAY DIFFRACTION' 1 ? ? ? ? ? ? 1 'loose positional' B 1122 0.38 5.00 2 'X-RAY DIFFRACTION' 2 ? ? ? ? ? ? 1 'loose thermal' A 376 0.40 10.00 1 'X-RAY DIFFRACTION' 3 ? ? ? ? ? ? 1 'loose thermal' B 1122 0.44 10.00 2 'X-RAY DIFFRACTION' 4 ? ? ? ? ? ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 3.300 _refine_ls_shell.d_res_low 3.383 _refine_ls_shell.number_reflns_R_work 568 _refine_ls_shell.R_factor_R_work 0.326 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.297 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 35 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _struct_ncs_dom.pdbx_ens_id _struct_ncs_dom.id _struct_ncs_dom.details 1 1 A 1 2 C 2 1 B 2 2 D # loop_ _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_comp_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.selection_details 1 1 1 E DAI . . A C 11 . A DAI 100 A C 111 6 ? 1 2 1 J DAI . . C C 11 . C DAI 100 C C 111 6 ? 2 1 1 B G 1 . B C 38 . B G 201 B C 238 6 ? 2 2 1 D G 1 . D C 38 . D G 201 D C 238 6 ? # loop_ _struct_ncs_ens.id _struct_ncs_ens.details _struct_ncs_ens.point_group 1 ? ? 2 ? ? # _struct.entry_id 1YKV _struct.title ;Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YKV _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'carbon-carbon bond, catalytic mechanism, Diels-Alder reaction, ribozyme, 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 1 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 4 ? J N N 3 ? K N N 4 ? L N N 4 ? M N N 4 ? # loop_ _struct_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 2 ? ? # 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 metalc1 metalc ? ? B G 13 OP1 ? ? ? 1_555 I MG . MG ? ? B G 213 B MG 246 1_555 ? ? ? ? ? ? ? 2.144 ? ? metalc2 metalc ? ? B A 16 OP2 ? ? ? 1_555 H MG . MG ? ? B A 216 B MG 242 1_555 ? ? ? ? ? ? ? 2.067 ? ? metalc3 metalc ? ? B C 33 OP2 ? ? ? 1_555 G MG . MG ? ? B C 233 B MG 241 1_555 ? ? ? ? ? ? ? 2.167 ? ? metalc4 metalc ? ? B U 34 OP1 ? ? ? 1_555 F MG . MG ? ? B U 234 B MG 240 1_555 ? ? ? ? ? ? ? 2.273 ? ? metalc5 metalc ? ? I MG . MG ? ? ? 1_555 D G 13 OP1 ? ? B MG 246 D G 213 1_555 ? ? ? ? ? ? ? 2.034 ? ? metalc6 metalc ? ? D A 16 OP2 ? ? ? 1_555 M MG . MG ? ? D A 216 D MG 342 1_555 ? ? ? ? ? ? ? 2.110 ? ? metalc7 metalc ? ? D C 33 OP2 ? ? ? 1_555 L MG . MG ? ? D C 233 D MG 341 1_555 ? ? ? ? ? ? ? 2.148 ? ? metalc8 metalc ? ? D U 34 OP1 ? ? ? 1_555 K MG . MG ? ? D U 234 D MG 340 1_555 ? ? ? ? ? ? ? 2.162 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 101 B C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 101 B C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 101 B C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 14 N3 ? ? A G 102 B C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 14 O2 ? ? A G 102 B C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 14 N4 ? ? A G 102 B C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 34 N3 ? ? A A 103 B U 234 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 34 O4 ? ? A A 103 B U 234 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 33 N3 ? ? A G 104 B C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 33 O2 ? ? A G 104 B C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 33 N4 ? ? A G 104 B C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 105 B G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 105 B G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 105 B G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 6 N1 ? ? A U 106 B A 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 6 N6 ? ? A U 106 B A 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 107 B G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 107 B G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 107 B G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 108 B C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 108 B C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 108 B C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 109 B G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 109 B G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 109 B G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 110 B G 201 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog27 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 110 B G 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 110 B G 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 110 B G 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 111 B G 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 111 B G 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 111 B G 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B G 8 N1 ? ? ? 1_555 B C 38 N3 ? ? B G 208 B C 238 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B G 8 N2 ? ? ? 1_555 B C 38 O2 ? ? B G 208 B C 238 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 8 O6 ? ? ? 1_555 B C 38 N4 ? ? B G 208 B C 238 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B C 9 N3 ? ? ? 1_555 B G 37 N1 ? ? B C 209 B G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B C 9 N4 ? ? ? 1_555 B G 37 O6 ? ? B C 209 B G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B C 9 O2 ? ? ? 1_555 B G 37 N2 ? ? B C 209 B G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B C 10 N3 ? ? ? 1_555 B G 36 N1 ? ? B C 210 B G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B C 10 N4 ? ? ? 1_555 B G 36 O6 ? ? B C 210 B G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B C 10 O2 ? ? ? 1_555 B G 36 N2 ? ? B C 210 B G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B G 11 N1 ? ? ? 1_555 B C 35 N3 ? ? B G 211 B C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B G 11 N2 ? ? ? 1_555 B C 35 O2 ? ? B G 211 B C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B G 11 O6 ? ? ? 1_555 B C 35 N4 ? ? B G 211 B C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? B U 12 N3 ? ? ? 1_555 B A 32 N7 ? ? B U 212 B A 232 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog46 hydrog ? ? B U 12 O2 ? ? ? 1_555 B A 32 N6 ? ? B U 212 B A 232 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog47 hydrog ? ? B C 14 N4 ? ? ? 1_555 B U 31 O2 ? ? B C 214 B U 231 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog48 hydrog ? ? B G 17 N1 ? ? ? 1_555 B C 28 N3 ? ? B G 217 B C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? B G 17 N2 ? ? ? 1_555 B C 28 O2 ? ? B G 217 B C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? B G 17 O6 ? ? ? 1_555 B C 28 N4 ? ? B G 217 B C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? B C 18 N3 ? ? ? 1_555 B G 27 N1 ? ? B C 218 B G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? B C 18 N4 ? ? ? 1_555 B G 27 O6 ? ? B C 218 B G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? B C 18 O2 ? ? ? 1_555 B G 27 N2 ? ? B C 218 B G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? B U 19 N3 ? ? ? 1_555 B A 26 N1 ? ? B U 219 B A 226 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B U 19 O4 ? ? ? 1_555 B A 26 N6 ? ? B U 219 B A 226 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B C 20 N3 ? ? ? 1_555 B G 25 N1 ? ? B C 220 B G 225 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B C 20 N4 ? ? ? 1_555 B G 25 O6 ? ? B C 220 B G 225 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B C 20 O2 ? ? ? 1_555 B G 25 N2 ? ? B C 220 B G 225 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B U 21 O2 ? ? ? 1_555 B G 24 N2 ? ? B U 221 B G 224 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog60 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 15 N3 ? ? C G 101 D C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 15 O2 ? ? C G 101 D C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 15 N4 ? ? C G 101 D C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 14 N3 ? ? C G 102 D C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C G 2 N2 ? ? ? 1_555 D C 14 O2 ? ? C G 102 D C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? C G 2 O6 ? ? ? 1_555 D C 14 N4 ? ? C G 102 D C 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? C A 3 N1 ? ? ? 1_555 D U 34 N3 ? ? C A 103 D U 234 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? C A 3 N6 ? ? ? 1_555 D U 34 O4 ? ? C A 103 D U 234 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 33 N3 ? ? C G 104 D C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? C G 4 N2 ? ? ? 1_555 D C 33 O2 ? ? C G 104 D C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? C G 4 O6 ? ? ? 1_555 D C 33 N4 ? ? C G 104 D C 233 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? C G 4 N1 ? ? ? 1_555 D U 34 O4 ? ? C G 104 D U 234 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog72 hydrog ? ? C C 5 N3 ? ? ? 1_555 D G 7 N1 ? ? C C 105 D G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? C C 5 N4 ? ? ? 1_555 D G 7 O6 ? ? C C 105 D G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? C C 5 O2 ? ? ? 1_555 D G 7 N2 ? ? C C 105 D G 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? C U 6 N3 ? ? ? 1_555 D A 6 N1 ? ? C U 106 D A 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? C U 6 O4 ? ? ? 1_555 D A 6 N6 ? ? C U 106 D A 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? C C 7 N3 ? ? ? 1_555 D G 5 N1 ? ? C C 107 D G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? C C 7 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 107 D G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? C C 7 O2 ? ? ? 1_555 D G 5 N2 ? ? C C 107 D G 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? C G 8 N1 ? ? ? 1_555 D C 4 N3 ? ? C G 108 D C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? C G 8 N2 ? ? ? 1_555 D C 4 O2 ? ? C G 108 D C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? C G 8 O6 ? ? ? 1_555 D C 4 N4 ? ? C G 108 D C 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? C C 9 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 109 D G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? C C 9 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 109 D G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? C C 9 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 109 D G 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? C C 10 N3 ? ? ? 1_555 D G 2 N1 ? ? C C 110 D G 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? C C 10 N4 ? ? ? 1_555 D G 2 O6 ? ? C C 110 D G 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? C C 10 O2 ? ? ? 1_555 D G 2 N2 ? ? C C 110 D G 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? C C 11 N3 ? ? ? 1_555 D G 1 N1 ? ? C C 111 D G 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? C C 11 N4 ? ? ? 1_555 D G 1 O6 ? ? C C 111 D G 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? C C 11 O2 ? ? ? 1_555 D G 1 N2 ? ? C C 111 D G 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog92 hydrog ? ? D G 8 N1 ? ? ? 1_555 D C 38 N3 ? ? D G 208 D C 238 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog93 hydrog ? ? D G 8 N2 ? ? ? 1_555 D C 38 O2 ? ? D G 208 D C 238 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog94 hydrog ? ? D G 8 O6 ? ? ? 1_555 D C 38 N4 ? ? D G 208 D C 238 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog95 hydrog ? ? D C 9 N3 ? ? ? 1_555 D G 37 N1 ? ? D C 209 D G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog96 hydrog ? ? D C 9 N4 ? ? ? 1_555 D G 37 O6 ? ? D C 209 D G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog97 hydrog ? ? D C 9 O2 ? ? ? 1_555 D G 37 N2 ? ? D C 209 D G 237 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog98 hydrog ? ? D C 10 N3 ? ? ? 1_555 D G 36 N1 ? ? D C 210 D G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog99 hydrog ? ? D C 10 N4 ? ? ? 1_555 D G 36 O6 ? ? D C 210 D G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog100 hydrog ? ? D C 10 O2 ? ? ? 1_555 D G 36 N2 ? ? D C 210 D G 236 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog101 hydrog ? ? D G 11 N1 ? ? ? 1_555 D C 35 N3 ? ? D G 211 D C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog102 hydrog ? ? D G 11 N2 ? ? ? 1_555 D C 35 O2 ? ? D G 211 D C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog103 hydrog ? ? D G 11 O6 ? ? ? 1_555 D C 35 N4 ? ? D G 211 D C 235 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog104 hydrog ? ? D U 12 N3 ? ? ? 1_555 D A 32 N7 ? ? D U 212 D A 232 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog105 hydrog ? ? D C 14 N4 ? ? ? 1_555 D U 31 O2 ? ? D C 214 D U 231 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog106 hydrog ? ? D A 16 N6 ? ? ? 1_555 D A 29 N1 ? ? D A 216 D A 229 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog107 hydrog ? ? D G 17 N1 ? ? ? 1_555 D C 28 N3 ? ? D G 217 D C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog108 hydrog ? ? D G 17 N2 ? ? ? 1_555 D C 28 O2 ? ? D G 217 D C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog109 hydrog ? ? D G 17 O6 ? ? ? 1_555 D C 28 N4 ? ? D G 217 D C 228 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog110 hydrog ? ? D C 18 N3 ? ? ? 1_555 D G 27 N1 ? ? D C 218 D G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog111 hydrog ? ? D C 18 N4 ? ? ? 1_555 D G 27 O6 ? ? D C 218 D G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog112 hydrog ? ? D C 18 O2 ? ? ? 1_555 D G 27 N2 ? ? D C 218 D G 227 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog113 hydrog ? ? D U 19 N3 ? ? ? 1_555 D A 26 N1 ? ? D U 219 D A 226 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog114 hydrog ? ? D U 19 O4 ? ? ? 1_555 D A 26 N6 ? ? D U 219 D A 226 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog115 hydrog ? ? D C 20 O2 ? ? ? 1_555 D G 25 N2 ? ? D C 220 D G 225 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog116 hydrog ? ? D U 21 O2 ? ? ? 1_555 D G 24 N1 ? ? D U 221 D G 224 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 B MG 240 ? 1 'BINDING SITE FOR RESIDUE MG B 240' AC2 Software B MG 241 ? 1 'BINDING SITE FOR RESIDUE MG B 241' AC3 Software B MG 242 ? 2 'BINDING SITE FOR RESIDUE MG B 242' AC4 Software B MG 246 ? 2 'BINDING SITE FOR RESIDUE MG B 246' AC5 Software D MG 340 ? 1 'BINDING SITE FOR RESIDUE MG D 340' AC6 Software D MG 341 ? 2 'BINDING SITE FOR RESIDUE MG D 341' AC7 Software D MG 342 ? 2 'BINDING SITE FOR RESIDUE MG D 342' AC8 Software A DAI 100 ? 7 'BINDING SITE FOR RESIDUE DAI A 100' AC9 Software C DAI 100 ? 8 'BINDING SITE FOR RESIDUE DAI C 100' # 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 1 U B 34 ? U B 234 . ? 1_555 ? 2 AC2 1 C B 33 ? C B 233 . ? 1_555 ? 3 AC3 2 A B 16 ? A B 216 . ? 1_555 ? 4 AC3 2 G B 17 ? G B 217 . ? 1_555 ? 5 AC4 2 G B 13 ? G B 213 . ? 1_555 ? 6 AC4 2 G D 13 ? G D 213 . ? 1_555 ? 7 AC5 1 U D 34 ? U D 234 . ? 1_555 ? 8 AC6 2 C D 10 ? C D 210 . ? 1_555 ? 9 AC6 2 C D 33 ? C D 233 . ? 1_555 ? 10 AC7 2 A D 16 ? A D 216 . ? 1_555 ? 11 AC7 2 G D 17 ? G D 217 . ? 1_555 ? 12 AC8 7 G A 2 ? G A 102 . ? 1_555 ? 13 AC8 7 A A 3 ? A A 103 . ? 1_555 ? 14 AC8 7 G B 13 ? G B 213 . ? 1_555 ? 15 AC8 7 C B 14 ? C B 214 . ? 1_555 ? 16 AC8 7 U B 31 ? U B 231 . ? 1_555 ? 17 AC8 7 A B 32 ? A B 232 . ? 1_555 ? 18 AC8 7 U B 34 ? U B 234 . ? 1_555 ? 19 AC9 8 U B 12 ? U B 212 . ? 1_555 ? 20 AC9 8 G C 2 ? G C 102 . ? 1_555 ? 21 AC9 8 A C 3 ? A C 103 . ? 1_555 ? 22 AC9 8 G D 13 ? G D 213 . ? 1_555 ? 23 AC9 8 C D 14 ? C D 214 . ? 1_555 ? 24 AC9 8 U D 31 ? U D 231 . ? 1_555 ? 25 AC9 8 A D 32 ? A D 232 . ? 1_555 ? 26 AC9 8 U D 34 ? U D 234 . ? 1_555 ? # _database_PDB_matrix.entry_id 1YKV _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1YKV _atom_sites.fract_transf_matrix[1][1] 0.012773 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.003874 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022707 _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] 0.013062 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 101 101 G G A . n A 1 2 G 2 102 102 G G A . n A 1 3 A 3 103 103 A A A . n A 1 4 G 4 104 104 G G A . n A 1 5 C 5 105 105 C C A . n A 1 6 U 6 106 106 U U A . n A 1 7 C 7 107 107 C C A . n A 1 8 G 8 108 108 G G A . n A 1 9 C 9 109 109 C C A . n A 1 10 C 10 110 110 C C A . n A 1 11 C 11 111 111 C C A . n B 2 1 G 1 201 201 G G B . n B 2 2 G 2 202 202 G G B . n B 2 3 G 3 203 203 G G B . n B 2 4 C 4 204 204 C C B . n B 2 5 G 5 205 205 G G B . n B 2 6 A 6 206 206 A A B . n B 2 7 G 7 207 207 G G B . n B 2 8 G 8 208 208 G G B . n B 2 9 C 9 209 209 C C B . n B 2 10 C 10 210 210 C C B . n B 2 11 G 11 211 211 G G B . n B 2 12 U 12 212 212 U U B . n B 2 13 G 13 213 213 G G B . n B 2 14 C 14 214 214 C C B . n B 2 15 C 15 215 215 C C B . n B 2 16 A 16 216 216 A A B . n B 2 17 G 17 217 217 G G B . n B 2 18 C 18 218 218 C C B . n B 2 19 U 19 219 219 U U B . n B 2 20 C 20 220 220 C C B . n B 2 21 U 21 221 221 U U B . n B 2 22 U 22 222 222 U U B . n B 2 23 C 23 223 223 C C B . n B 2 24 G 24 224 224 G G B . n B 2 25 G 25 225 225 G G B . n B 2 26 A 26 226 226 A A B . n B 2 27 G 27 227 227 G G B . n B 2 28 C 28 228 228 C C B . n B 2 29 A 29 229 229 A A B . n B 2 30 A 30 230 230 A A B . n B 2 31 U 31 231 231 U U B . n B 2 32 A 32 232 232 A A B . n B 2 33 C 33 233 233 C C B . n B 2 34 U 34 234 234 U U B . n B 2 35 C 35 235 235 C C B . n B 2 36 G 36 236 236 G G B . n B 2 37 G 37 237 237 G G B . n B 2 38 C 38 238 238 C C B . n C 1 1 G 1 101 101 G G C . n C 1 2 G 2 102 102 G G C . n C 1 3 A 3 103 103 A A C . n C 1 4 G 4 104 104 G G C . n C 1 5 C 5 105 105 C C C . n C 1 6 U 6 106 106 U U C . n C 1 7 C 7 107 107 C C C . n C 1 8 G 8 108 108 G G C . n C 1 9 C 9 109 109 C C C . n C 1 10 C 10 110 110 C C C . n C 1 11 C 11 111 111 C C C . n D 2 1 G 1 201 201 G G D . n D 2 2 G 2 202 202 G G D . n D 2 3 G 3 203 203 G G D . n D 2 4 C 4 204 204 C C D . n D 2 5 G 5 205 205 G G D . n D 2 6 A 6 206 206 A A D . n D 2 7 G 7 207 207 G G D . n D 2 8 G 8 208 208 G G D . n D 2 9 C 9 209 209 C C D . n D 2 10 C 10 210 210 C C D . n D 2 11 G 11 211 211 G G D . n D 2 12 U 12 212 212 U U D . n D 2 13 G 13 213 213 G G D . n D 2 14 C 14 214 214 C C D . n D 2 15 C 15 215 215 C C D . n D 2 16 A 16 216 216 A A D . n D 2 17 G 17 217 217 G G D . n D 2 18 C 18 218 218 C C D . n D 2 19 U 19 219 219 U U D . n D 2 20 C 20 220 220 C C D . n D 2 21 U 21 221 221 U U D . n D 2 22 U 22 222 222 U U D . n D 2 23 C 23 223 223 C C D . n D 2 24 G 24 224 224 G G D . n D 2 25 G 25 225 225 G G D . n D 2 26 A 26 226 226 A A D . n D 2 27 G 27 227 227 G G D . n D 2 28 C 28 228 228 C C D . n D 2 29 A 29 229 229 A A D . n D 2 30 A 30 230 230 A A D . n D 2 31 U 31 231 231 U U D . n D 2 32 A 32 232 232 A A D . n D 2 33 C 33 233 233 C C D . n D 2 34 U 34 234 234 U U D . n D 2 35 C 35 235 235 C C D . n D 2 36 G 36 236 236 G G D . n D 2 37 G 37 237 237 G G D . n D 2 38 C 38 238 238 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 3 DAI 1 100 100 DAI DAI A . F 4 MG 1 240 240 MG MG B . G 4 MG 1 241 241 MG MG B . H 4 MG 1 242 242 MG MG B . I 4 MG 1 246 246 MG MG B . J 3 DAI 1 100 100 DAI DAI C . K 4 MG 1 340 340 MG MG D . L 4 MG 1 341 341 MG MG D . M 4 MG 1 342 342 MG MG D . # 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_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # 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,G,H,I 2 1 C,D,J,K,L,M # _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 # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id OP1 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id B _pdbx_struct_conn_angle.ptnr1_label_comp_id G _pdbx_struct_conn_angle.ptnr1_label_seq_id 13 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id B _pdbx_struct_conn_angle.ptnr1_auth_comp_id G _pdbx_struct_conn_angle.ptnr1_auth_seq_id 213 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id MG _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id I _pdbx_struct_conn_angle.ptnr2_label_comp_id MG _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id B _pdbx_struct_conn_angle.ptnr2_auth_comp_id MG _pdbx_struct_conn_angle.ptnr2_auth_seq_id 246 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id OP1 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id D _pdbx_struct_conn_angle.ptnr3_label_comp_id G _pdbx_struct_conn_angle.ptnr3_label_seq_id 13 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id D _pdbx_struct_conn_angle.ptnr3_auth_comp_id G _pdbx_struct_conn_angle.ptnr3_auth_seq_id 213 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 80.9 _pdbx_struct_conn_angle.value_esd ? # 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 2005-02-22 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-23 # _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' 'Version format compliance' 2 3 'Structure model' Advisory 3 3 'Structure model' 'Refinement description' 4 3 'Structure model' 'Version format compliance' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Derived calculations' 8 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_ncs_dom_lim 7 4 'Structure model' struct_site # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_dist_value' 4 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 5 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 6 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 16 4 'Structure model' '_struct_ncs_dom_lim.beg_auth_comp_id' 17 4 'Structure model' '_struct_ncs_dom_lim.beg_label_asym_id' 18 4 'Structure model' '_struct_ncs_dom_lim.beg_label_seq_id' 19 4 'Structure model' '_struct_ncs_dom_lim.end_auth_comp_id' 20 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 21 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 22 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 28.2942 25.6012 34.0195 -0.0677 -0.1984 -0.1962 -0.0168 0.2104 0.1709 6.6386 2.6940 10.1018 -0.1901 -7.8845 -1.1824 -0.0329 0.6192 -0.5863 0.4567 0.3802 0.4655 0.1215 0.0320 -0.8974 'X-RAY DIFFRACTION' 2 ? refined 37.8218 26.7509 19.6474 -0.2742 -0.3025 -0.3375 -0.1219 -0.0152 0.0803 1.0523 4.0371 5.9779 -0.4020 -1.3101 0.6861 -0.0355 0.2839 -0.2484 0.1519 -0.0768 0.3478 -0.4317 0.2254 -0.0508 'X-RAY DIFFRACTION' 3 ? refined 65.8600 34.2810 33.9042 -0.0752 -0.2747 0.0883 -0.0343 -0.2325 -0.1567 10.1130 2.2998 9.6968 -0.6807 8.4752 1.8477 -0.1707 0.4069 -0.2362 0.4862 0.2152 -0.5309 0.1066 0.1234 0.7441 'X-RAY DIFFRACTION' 4 ? refined 56.2401 33.4043 19.6050 -0.2679 -0.1949 -0.1198 -0.1455 -0.0531 -0.0477 1.2130 3.1080 5.5759 -1.6398 1.9151 -1.0809 0.0332 0.2310 -0.2642 0.3928 0.1433 -0.5544 -0.3802 -0.0975 0.4293 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 101 A 111 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 B 201 B 238 ? . . . . ? 'X-RAY DIFFRACTION' 3 3 C 101 C 111 ? . . . . ? 'X-RAY DIFFRACTION' 4 4 D 201 D 238 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.9999 ? 1 HKL-2000 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 AMoRE phasing . ? 4 # _pdbx_database_remark.id 999 _pdbx_database_remark.text ;SEQUENCE The DAI hetgroup is connected to the 5' G of the 11-mer RNA via hexaethyleneglycol linker. The linker is not visible in the electron density. ; # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 A _pdbx_validate_rmsd_bond.auth_seq_id_1 230 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C5'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 A _pdbx_validate_rmsd_bond.auth_seq_id_2 230 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.358 _pdbx_validate_rmsd_bond.bond_target_value 1.420 _pdbx_validate_rmsd_bond.bond_deviation -0.062 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.009 _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 "O4'" B G 201 ? ? "C4'" B G 201 ? ? "C3'" B G 201 ? ? 96.46 104.00 -7.54 1.00 N 2 1 "C1'" B G 201 ? ? "O4'" B G 201 ? ? "C4'" B G 201 ? ? 115.57 109.90 5.67 0.80 N 3 1 "C1'" B G 207 ? ? "O4'" B G 207 ? ? "C4'" B G 207 ? ? 105.28 109.70 -4.42 0.70 N 4 1 "O4'" B U 222 ? ? "C1'" B U 222 ? ? N1 B U 222 ? ? 113.50 108.50 5.00 0.70 N 5 1 "O4'" B U 234 ? ? "C1'" B U 234 ? ? N1 B U 234 ? ? 103.30 108.20 -4.90 0.80 N 6 1 "O4'" D G 201 ? ? "C4'" D G 201 ? ? "C3'" D G 201 ? ? 95.88 104.00 -8.12 1.00 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 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 DAI O23 O N N 73 DAI C24 C N N 74 DAI C28 C N S 75 DAI C13 C N N 76 DAI C15 C Y N 77 DAI C16 C Y N 78 DAI C17 C Y N 79 DAI C18 C Y N 80 DAI C19 C Y N 81 DAI C14 C Y N 82 DAI C12 C Y N 83 DAI C11 C Y N 84 DAI C9 C Y N 85 DAI C8 C Y N 86 DAI C7 C Y N 87 DAI C6 C Y N 88 DAI C27 C N S 89 DAI C10 C N N 90 DAI C5 C N N 91 DAI O4 O N N 92 DAI C26 C N N 93 DAI O22 O N N 94 DAI N25 N N N 95 DAI C21 C N N 96 DAI C20 C N N 97 DAI C3 C N N 98 DAI C2 C N N 99 DAI C1 C N N 100 DAI H28 H N N 101 DAI H13 H N N 102 DAI H17 H N N 103 DAI H18 H N N 104 DAI H19 H N N 105 DAI H14 H N N 106 DAI H9 H N N 107 DAI H8 H N N 108 DAI H7 H N N 109 DAI H6 H N N 110 DAI H27 H N N 111 DAI H51 H N N 112 DAI H52 H N N 113 DAI HO4 H N N 114 DAI H211 H N N 115 DAI H212 H N N 116 DAI H201 H N N 117 DAI H202 H N N 118 DAI H31 H N N 119 DAI H32 H N N 120 DAI H21 H N N 121 DAI H22 H N N 122 DAI H11 H N N 123 DAI H12 H N N 124 DAI H13A H N N 125 G OP3 O N N 126 G P P N N 127 G OP1 O N N 128 G OP2 O N N 129 G "O5'" O N N 130 G "C5'" C N N 131 G "C4'" C N R 132 G "O4'" O N N 133 G "C3'" C N S 134 G "O3'" O N N 135 G "C2'" C N R 136 G "O2'" O N N 137 G "C1'" C N R 138 G N9 N Y N 139 G C8 C Y N 140 G N7 N Y N 141 G C5 C Y N 142 G C6 C N N 143 G O6 O N N 144 G N1 N N N 145 G C2 C N N 146 G N2 N N N 147 G N3 N N N 148 G C4 C Y N 149 G HOP3 H N N 150 G HOP2 H N N 151 G "H5'" H N N 152 G "H5''" H N N 153 G "H4'" H N N 154 G "H3'" H N N 155 G "HO3'" H N N 156 G "H2'" H N N 157 G "HO2'" H N N 158 G "H1'" H N N 159 G H8 H N N 160 G H1 H N N 161 G H21 H N N 162 G H22 H N N 163 MG MG MG N N 164 U OP3 O N N 165 U P P N N 166 U OP1 O N N 167 U OP2 O N N 168 U "O5'" O N N 169 U "C5'" C N N 170 U "C4'" C N R 171 U "O4'" O N N 172 U "C3'" C N S 173 U "O3'" O N N 174 U "C2'" C N R 175 U "O2'" O N N 176 U "C1'" C N R 177 U N1 N N N 178 U C2 C N N 179 U O2 O N N 180 U N3 N N N 181 U C4 C N N 182 U O4 O N N 183 U C5 C N N 184 U C6 C N N 185 U HOP3 H N N 186 U HOP2 H N N 187 U "H5'" H N N 188 U "H5''" H N N 189 U "H4'" H N N 190 U "H3'" H N N 191 U "HO3'" H N N 192 U "H2'" H N N 193 U "HO2'" H N N 194 U "H1'" H N N 195 U H3 H N N 196 U H5 H N N 197 U H6 H N N 198 # 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 DAI O23 C24 doub N N 76 DAI C24 C28 sing N N 77 DAI C24 N25 sing N N 78 DAI C28 C13 sing N N 79 DAI C28 C27 sing N N 80 DAI C28 H28 sing N N 81 DAI C13 C15 sing N N 82 DAI C13 C12 sing N N 83 DAI C13 H13 sing N N 84 DAI C15 C16 doub Y N 85 DAI C15 C14 sing Y N 86 DAI C16 C17 sing Y N 87 DAI C16 C10 sing N N 88 DAI C17 C18 doub Y N 89 DAI C17 H17 sing N N 90 DAI C18 C19 sing Y N 91 DAI C18 H18 sing N N 92 DAI C19 C14 doub Y N 93 DAI C19 H19 sing N N 94 DAI C14 H14 sing N N 95 DAI C12 C11 doub Y N 96 DAI C12 C6 sing Y N 97 DAI C11 C9 sing Y N 98 DAI C11 C10 sing N N 99 DAI C9 C8 doub Y N 100 DAI C9 H9 sing N N 101 DAI C8 C7 sing Y N 102 DAI C8 H8 sing N N 103 DAI C7 C6 doub Y N 104 DAI C7 H7 sing N N 105 DAI C6 H6 sing N N 106 DAI C27 C10 sing N N 107 DAI C27 C26 sing N N 108 DAI C27 H27 sing N N 109 DAI C10 C5 sing N N 110 DAI C5 O4 sing N N 111 DAI C5 H51 sing N N 112 DAI C5 H52 sing N N 113 DAI O4 HO4 sing N N 114 DAI C26 O22 doub N N 115 DAI C26 N25 sing N N 116 DAI N25 C21 sing N N 117 DAI C21 C20 sing N N 118 DAI C21 H211 sing N N 119 DAI C21 H212 sing N N 120 DAI C20 C3 sing N N 121 DAI C20 H201 sing N N 122 DAI C20 H202 sing N N 123 DAI C3 C2 sing N N 124 DAI C3 H31 sing N N 125 DAI C3 H32 sing N N 126 DAI C2 C1 sing N N 127 DAI C2 H21 sing N N 128 DAI C2 H22 sing N N 129 DAI C1 H11 sing N N 130 DAI C1 H12 sing N N 131 DAI C1 H13A sing N N 132 G OP3 P sing N N 133 G OP3 HOP3 sing N N 134 G P OP1 doub N N 135 G P OP2 sing N N 136 G P "O5'" sing N N 137 G OP2 HOP2 sing N N 138 G "O5'" "C5'" sing N N 139 G "C5'" "C4'" sing N N 140 G "C5'" "H5'" sing N N 141 G "C5'" "H5''" sing N N 142 G "C4'" "O4'" sing N N 143 G "C4'" "C3'" sing N N 144 G "C4'" "H4'" sing N N 145 G "O4'" "C1'" sing N N 146 G "C3'" "O3'" sing N N 147 G "C3'" "C2'" sing N N 148 G "C3'" "H3'" sing N N 149 G "O3'" "HO3'" sing N N 150 G "C2'" "O2'" sing N N 151 G "C2'" "C1'" sing N N 152 G "C2'" "H2'" sing N N 153 G "O2'" "HO2'" sing N N 154 G "C1'" N9 sing N N 155 G "C1'" "H1'" sing N N 156 G N9 C8 sing Y N 157 G N9 C4 sing Y N 158 G C8 N7 doub Y N 159 G C8 H8 sing N N 160 G N7 C5 sing Y N 161 G C5 C6 sing N N 162 G C5 C4 doub Y N 163 G C6 O6 doub N N 164 G C6 N1 sing N N 165 G N1 C2 sing N N 166 G N1 H1 sing N N 167 G C2 N2 sing N N 168 G C2 N3 doub N N 169 G N2 H21 sing N N 170 G N2 H22 sing N N 171 G N3 C4 sing N N 172 U OP3 P sing N N 173 U OP3 HOP3 sing N N 174 U P OP1 doub N N 175 U P OP2 sing N N 176 U P "O5'" sing N N 177 U OP2 HOP2 sing N N 178 U "O5'" "C5'" sing N N 179 U "C5'" "C4'" sing N N 180 U "C5'" "H5'" sing N N 181 U "C5'" "H5''" sing N N 182 U "C4'" "O4'" sing N N 183 U "C4'" "C3'" sing N N 184 U "C4'" "H4'" sing N N 185 U "O4'" "C1'" sing N N 186 U "C3'" "O3'" sing N N 187 U "C3'" "C2'" sing N N 188 U "C3'" "H3'" sing N N 189 U "O3'" "HO3'" sing N N 190 U "C2'" "O2'" sing N N 191 U "C2'" "C1'" sing N N 192 U "C2'" "H2'" sing N N 193 U "O2'" "HO2'" sing N N 194 U "C1'" N1 sing N N 195 U "C1'" "H1'" sing N N 196 U N1 C2 sing N N 197 U N1 C6 sing N N 198 U C2 O2 doub N N 199 U C2 N3 sing N N 200 U N3 C4 sing N N 201 U N3 H3 sing N N 202 U C4 O4 doub N N 203 U C4 C5 sing N N 204 U C5 C6 doub N N 205 U C5 H5 sing N N 206 U C6 H6 sing N N 207 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1YKV 'double helix' 1YKV 'a-form double helix' 1YKV tetraloop 1YKV 'bulge loop' 1YKV 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 15 1_555 1.163 0.000 -0.042 -8.795 -4.017 5.090 1 A_G101:C215_B A 101 ? B 215 ? 19 1 1 A G 2 1_555 B C 14 1_555 -0.106 -0.041 0.099 -8.390 -7.600 -1.203 2 A_G102:C214_B A 102 ? B 214 ? 19 1 1 A A 3 1_555 B U 34 1_555 -0.099 -0.176 -0.884 -10.172 0.395 -1.886 3 A_A103:U234_B A 103 ? B 234 ? 20 1 1 A G 4 1_555 B C 33 1_555 -0.704 -0.118 -0.123 -9.813 -8.746 6.615 4 A_G104:C233_B A 104 ? B 233 ? 19 1 1 A C 5 1_555 B G 7 1_555 -0.355 -0.183 0.012 2.975 -6.897 -1.140 5 A_C105:G207_B A 105 ? B 207 ? 19 1 1 A U 6 1_555 B A 6 1_555 -0.571 -0.153 0.350 10.083 -4.732 10.201 6 A_U106:A206_B A 106 ? B 206 ? 20 1 1 A C 7 1_555 B G 5 1_555 -0.055 -0.092 0.097 8.598 -16.277 4.996 7 A_C107:G205_B A 107 ? B 205 ? 19 1 1 A G 8 1_555 B C 4 1_555 0.977 -0.165 0.434 3.772 -12.642 -19.440 8 A_G108:C204_B A 108 ? B 204 ? 19 1 1 A C 9 1_555 B G 3 1_555 -0.044 -0.379 0.821 -3.903 -10.639 -1.220 9 A_C109:G203_B A 109 ? B 203 ? 19 1 1 A C 10 1_555 B G 2 1_555 0.203 -0.201 0.684 -9.820 -14.228 -0.243 10 A_C110:G202_B A 110 ? B 202 ? 19 1 1 A C 11 1_555 B G 1 1_555 0.080 -0.027 0.821 -4.259 -5.969 -5.180 11 A_C111:G201_B A 111 ? B 201 ? 19 1 1 B G 8 1_555 B C 38 1_555 -0.262 0.039 0.294 13.394 -7.183 0.375 12 B_G208:C238_B B 208 ? B 238 ? 19 1 1 B C 9 1_555 B G 37 1_555 -0.012 -0.304 -0.923 16.163 -22.109 1.385 13 B_C209:G237_B B 209 ? B 237 ? 19 1 1 B C 10 1_555 B G 36 1_555 -0.549 -0.202 0.329 -6.507 -2.321 0.541 14 B_C210:G236_B B 210 ? B 236 ? 19 1 1 B G 11 1_555 B C 35 1_555 -0.928 -0.276 0.406 3.233 -19.165 -0.064 15 B_G211:C235_B B 211 ? B 235 ? 19 1 1 B U 12 1_555 B A 32 1_555 4.122 -1.759 0.905 -6.227 7.334 -96.316 16 B_U212:A232_B B 212 ? B 232 ? 24 4 1 B G 17 1_555 B C 28 1_555 -0.050 -0.001 0.586 20.026 -8.221 -5.904 17 B_G217:C228_B B 217 ? B 228 ? 19 1 1 B C 18 1_555 B G 27 1_555 0.111 -0.117 0.029 13.020 -18.008 5.287 18 B_C218:G227_B B 218 ? B 227 ? 19 1 1 B U 19 1_555 B A 26 1_555 0.140 -0.010 0.215 8.617 -4.239 8.369 19 B_U219:A226_B B 219 ? B 226 ? 20 1 1 B C 20 1_555 B G 25 1_555 0.293 -0.107 0.096 -0.449 -7.897 2.633 20 B_C220:G225_B B 220 ? B 225 ? 19 1 1 B U 21 1_555 B G 24 1_555 0.448 -6.646 0.830 -17.865 1.461 -126.127 21 B_U221:G224_B B 221 ? B 224 ? ? ? 1 D C 14 1_555 C G 2 1_555 -0.167 -0.134 0.017 4.516 -4.656 1.011 22 D_C214:G102_C D 214 ? C 102 ? 19 1 1 D C 15 1_555 C G 1 1_555 -0.869 -0.025 0.354 8.536 -10.725 -3.317 23 D_C215:G101_C D 215 ? C 101 ? 19 1 1 D A 16 1_555 D A 29 1_555 -1.797 2.411 0.295 19.568 -7.046 -47.582 24 D_A216:A229_D D 216 ? D 229 ? ? ? 1 D G 17 1_555 D C 28 1_555 0.874 -0.022 0.382 12.705 -12.054 0.784 25 D_G217:C228_D D 217 ? D 228 ? 19 1 1 D C 18 1_555 D G 27 1_555 0.132 -0.326 -0.212 9.304 -15.231 3.921 26 D_C218:G227_D D 218 ? D 227 ? 19 1 1 D U 19 1_555 D A 26 1_555 -0.087 -0.195 0.156 -2.097 6.082 2.188 27 D_U219:A226_D D 219 ? D 226 ? 20 1 1 D C 20 1_555 D G 25 1_555 -0.626 0.315 -0.241 8.995 -2.268 14.379 28 D_C220:G225_D D 220 ? D 225 ? ? 1 1 D U 21 1_555 D G 24 1_555 1.372 -5.396 -0.025 -10.088 -0.099 -107.951 29 D_U221:G224_D D 221 ? D 224 ? ? ? 1 C A 3 1_555 D U 34 1_555 -0.108 -0.308 -1.389 -18.170 -8.190 -4.699 30 C_A103:U234_D C 103 ? D 234 ? 20 1 1 C G 4 1_555 D C 33 1_555 0.287 -0.004 -0.115 -7.843 -0.570 2.416 31 C_G104:C233_D C 104 ? D 233 ? 19 1 1 C C 5 1_555 D G 7 1_555 0.088 -0.258 -0.006 1.265 -18.181 -1.069 32 C_C105:G207_D C 105 ? D 207 ? 19 1 1 C U 6 1_555 D A 6 1_555 -0.138 0.011 0.433 9.755 -7.687 11.204 33 C_U106:A206_D C 106 ? D 206 ? 20 1 1 C C 7 1_555 D G 5 1_555 -0.565 -0.320 0.609 2.757 -10.019 -3.621 34 C_C107:G205_D C 107 ? D 205 ? 19 1 1 C G 8 1_555 D C 4 1_555 0.016 -0.017 0.293 -2.607 -6.738 -4.148 35 C_G108:C204_D C 108 ? D 204 ? 19 1 1 C C 9 1_555 D G 3 1_555 -0.179 -0.205 0.446 -3.215 -6.864 -1.670 36 C_C109:G203_D C 109 ? D 203 ? 19 1 1 C C 10 1_555 D G 2 1_555 0.118 -0.148 0.491 -8.789 -9.395 2.802 37 C_C110:G202_D C 110 ? D 202 ? 19 1 1 C C 11 1_555 D G 1 1_555 0.077 -0.079 1.078 -12.544 -2.897 -3.371 38 C_C111:G201_D C 111 ? D 201 ? 19 1 1 D G 8 1_555 D C 38 1_555 -0.171 -0.034 -0.057 5.933 -7.135 -0.089 39 D_G208:C238_D D 208 ? D 238 ? 19 1 1 D C 9 1_555 D G 37 1_555 0.247 -0.169 -0.686 18.002 -10.450 0.993 40 D_C209:G237_D D 209 ? D 237 ? 19 1 1 D C 10 1_555 D G 36 1_555 -0.274 0.068 -0.742 6.259 -8.564 10.712 41 D_C210:G236_D D 210 ? D 236 ? 19 1 1 D G 11 1_555 D C 35 1_555 -0.750 0.075 0.355 -7.488 -16.096 -3.134 42 D_G211:C235_D D 211 ? D 235 ? 19 1 1 D U 12 1_555 D A 32 1_555 4.467 -1.744 1.100 1.495 8.927 -103.026 43 D_U212:A232_D D 212 ? D 232 ? ? ? # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 15 1_555 A G 2 1_555 B C 14 1_555 -0.700 -2.076 3.087 2.859 2.203 30.339 -4.339 1.845 2.856 4.191 -5.438 30.548 1 AA_G101G102:C214C215_BB A 101 ? B 215 ? A 102 ? B 214 ? 1 A A 3 1_555 B U 34 1_555 A G 4 1_555 B C 33 1_555 1.267 -1.430 3.231 -1.026 8.190 28.771 -4.337 -2.652 2.685 16.069 2.014 29.908 2 AA_A103G104:C233U234_BB A 103 ? B 234 ? A 104 ? B 233 ? 1 A G 4 1_555 B C 33 1_555 A C 5 1_555 B G 7 1_555 -1.142 -2.607 2.735 -1.903 5.466 22.426 -7.933 2.346 2.135 13.763 4.791 23.151 3 AA_G104C105:G207C233_BB A 104 ? B 233 ? A 105 ? B 207 ? 1 A C 5 1_555 B G 7 1_555 A U 6 1_555 B A 6 1_555 -0.374 -1.993 2.897 -9.113 14.075 25.881 -5.852 -0.652 1.658 27.994 18.124 30.760 4 AA_C105U106:A206G207_BB A 105 ? B 207 ? A 106 ? B 206 ? 1 A U 6 1_555 B A 6 1_555 A C 7 1_555 B G 5 1_555 -0.358 -1.157 3.193 0.826 2.839 34.082 -2.398 0.734 3.080 4.833 -1.406 34.207 5 AA_U106C107:G205A206_BB A 106 ? B 206 ? A 107 ? B 205 ? 1 A C 7 1_555 B G 5 1_555 A G 8 1_555 B C 4 1_555 -0.976 -2.251 3.129 -5.576 11.521 39.816 -4.232 0.850 2.520 16.411 7.942 41.743 6 AA_C107G108:C204G205_BB A 107 ? B 205 ? A 108 ? B 204 ? 1 A G 8 1_555 B C 4 1_555 A C 9 1_555 B G 3 1_555 0.628 -1.655 3.276 -2.424 4.700 26.275 -4.725 -1.952 2.873 10.207 5.265 26.792 7 AA_G108C109:G203C204_BB A 108 ? B 204 ? A 109 ? B 203 ? 1 A C 9 1_555 B G 3 1_555 A C 10 1_555 B G 2 1_555 -0.149 -1.650 3.064 3.498 6.038 37.338 -3.227 0.629 2.749 9.332 -5.406 37.962 8 AA_C109C110:G202G203_BB A 109 ? B 203 ? A 110 ? B 202 ? 1 A C 10 1_555 B G 2 1_555 A C 11 1_555 B G 1 1_555 0.228 -1.167 3.059 2.437 0.922 39.352 -1.830 -0.070 3.040 1.368 -3.615 39.435 9 AA_C110C111:G201G202_BB A 110 ? B 202 ? A 111 ? B 201 ? 1 B G 8 1_555 B C 38 1_555 B C 9 1_555 B G 37 1_555 -0.568 -1.951 3.234 3.406 -1.119 34.681 -3.088 1.460 3.224 -1.871 -5.694 34.860 10 BB_G208C209:G237C238_BB B 208 ? B 238 ? B 209 ? B 237 ? 1 B C 9 1_555 B G 37 1_555 B C 10 1_555 B G 36 1_555 -0.264 -1.862 4.007 -8.834 7.903 24.235 -6.335 -2.046 3.158 17.543 19.611 26.939 11 BB_C209C210:G236G237_BB B 209 ? B 237 ? B 210 ? B 236 ? 1 B C 10 1_555 B G 36 1_555 B G 11 1_555 B C 35 1_555 1.032 -1.882 2.586 1.477 12.006 32.272 -4.490 -1.583 1.834 20.713 -2.548 34.408 12 BB_C210G211:C235G236_BB B 210 ? B 236 ? B 211 ? B 235 ? 1 B G 11 1_555 B C 35 1_555 B U 12 1_555 B A 32 1_555 -2.720 -1.746 3.637 1.457 4.604 85.946 -1.393 2.029 3.521 3.375 -1.068 86.056 13 BB_G211U212:A232C235_BB B 211 ? B 235 ? B 212 ? B 232 ? 1 B G 17 1_555 B C 28 1_555 B C 18 1_555 B G 27 1_555 0.919 -1.970 3.323 2.896 -1.143 41.207 -2.665 -0.981 3.428 -1.621 -4.107 41.319 14 BB_G217C218:G227C228_BB B 217 ? B 228 ? B 218 ? B 227 ? 1 B C 18 1_555 B G 27 1_555 B U 19 1_555 B A 26 1_555 -0.031 -1.819 3.167 -1.163 8.897 32.046 -4.513 -0.121 2.582 15.734 2.057 33.247 15 BB_C218U219:A226G227_BB B 218 ? B 227 ? B 219 ? B 226 ? 1 B U 19 1_555 B A 26 1_555 B C 20 1_555 B G 25 1_555 0.412 -2.074 3.256 3.323 5.625 27.268 -5.532 -0.112 2.809 11.720 -6.924 28.026 16 BB_U219C220:G225A226_BB B 219 ? B 226 ? B 220 ? B 225 ? 1 B C 20 1_555 B G 25 1_555 B U 21 1_555 B G 24 1_555 -2.192 -0.780 3.401 8.469 8.570 103.939 -0.615 1.507 3.218 5.428 -5.364 104.433 17 BB_C220U221:G224G225_BB B 220 ? B 225 ? B 221 ? B 224 ? 1 D C 14 1_555 C G 2 1_555 D C 15 1_555 C G 1 1_555 0.194 -1.934 2.803 -3.008 4.592 36.312 -3.584 -0.644 2.525 7.317 4.792 36.711 18 DD_C214C215:G101G102_CC D 214 ? C 102 ? D 215 ? C 101 ? 1 D C 15 1_555 C G 1 1_555 D A 16 1_555 D A 29 1_555 3.525 -2.502 3.294 -7.021 -11.186 69.014 -1.775 -3.322 3.289 -9.782 6.140 70.113 19 DD_C215A216:A229G101_DC D 215 ? C 101 ? D 216 ? D 229 ? 1 D A 16 1_555 D A 29 1_555 D G 17 1_555 D C 28 1_555 2.083 -1.535 3.330 -5.112 7.931 41.673 -2.858 -3.345 2.744 10.980 7.077 42.681 20 DD_A216G217:C228A229_DD D 216 ? D 229 ? D 217 ? D 228 ? 1 D G 17 1_555 D C 28 1_555 D C 18 1_555 D G 27 1_555 -0.203 -1.835 3.088 -0.510 5.164 31.653 -4.158 0.285 2.764 9.388 0.927 32.065 21 DD_G217C218:G227C228_DD D 217 ? D 228 ? D 218 ? D 227 ? 1 D C 18 1_555 D G 27 1_555 D U 19 1_555 D A 26 1_555 -0.381 -2.240 3.534 -6.248 8.427 32.674 -5.139 -0.345 2.905 14.520 10.765 34.273 22 DD_C218U219:A226G227_DD D 218 ? D 227 ? D 219 ? D 226 ? 1 D U 19 1_555 D A 26 1_555 D C 20 1_555 D G 25 1_555 0.905 -1.539 2.917 4.146 0.363 24.410 -3.690 -0.965 3.004 0.851 -9.714 24.757 23 DD_U219C220:G225A226_DD D 219 ? D 226 ? D 220 ? D 225 ? 1 D C 20 1_555 D G 25 1_555 D U 21 1_555 D G 24 1_555 -1.651 -0.581 3.512 11.347 12.285 103.485 -0.549 1.212 3.312 7.788 -7.193 104.442 24 DD_C220U221:G224G225_DD D 220 ? D 225 ? D 221 ? D 224 ? 1 C A 3 1_555 D U 34 1_555 C G 4 1_555 D C 33 1_555 0.720 -1.338 3.012 -7.116 7.446 35.535 -2.975 -1.962 2.506 11.895 11.368 36.951 25 CC_A103G104:C233U234_DD C 103 ? D 234 ? C 104 ? D 233 ? 1 C G 4 1_555 D C 33 1_555 C C 5 1_555 D G 7 1_555 -1.351 -2.374 2.955 0.169 1.719 17.544 -8.642 4.497 2.698 5.619 -0.552 17.628 26 CC_G104C105:G207C233_DD C 104 ? D 233 ? C 105 ? D 207 ? 1 C C 5 1_555 D G 7 1_555 C U 6 1_555 D A 6 1_555 -0.418 -1.848 2.933 -10.015 13.008 27.874 -5.181 -0.677 1.939 24.499 18.862 32.266 27 CC_C105U106:A206G207_DD C 105 ? D 207 ? C 106 ? D 206 ? 1 C U 6 1_555 D A 6 1_555 C C 7 1_555 D G 5 1_555 -0.391 -1.660 3.312 -3.772 2.139 26.728 -4.089 -0.122 3.196 4.588 8.092 27.071 28 CC_U106C107:G205A206_DD C 106 ? D 206 ? C 107 ? D 205 ? 1 C C 7 1_555 D G 5 1_555 C G 8 1_555 D C 4 1_555 -0.084 -1.654 2.970 0.305 10.141 37.275 -3.560 0.158 2.453 15.516 -0.466 38.584 29 CC_C107G108:C204G205_DD C 107 ? D 205 ? C 108 ? D 204 ? 1 C G 8 1_555 D C 4 1_555 C C 9 1_555 D G 3 1_555 -0.066 -1.808 3.127 -1.913 7.282 34.151 -4.002 -0.150 2.695 12.216 3.209 34.947 30 CC_G108C109:G203C204_DD C 108 ? D 204 ? C 109 ? D 203 ? 1 C C 9 1_555 D G 3 1_555 C C 10 1_555 D G 2 1_555 0.038 -1.573 3.116 0.693 3.285 36.929 -2.884 0.026 2.970 5.173 -1.092 37.076 31 CC_C109C110:G202G203_DD C 109 ? D 203 ? C 110 ? D 202 ? 1 C C 10 1_555 D G 2 1_555 C C 11 1_555 D G 1 1_555 0.004 -1.201 3.361 1.133 4.995 39.210 -2.366 0.128 3.190 7.405 -1.680 39.530 32 CC_C110C111:G201G202_DD C 110 ? D 202 ? C 111 ? D 201 ? 1 D G 8 1_555 D C 38 1_555 D C 9 1_555 D G 37 1_555 -0.500 -1.988 3.099 -2.350 -4.984 37.071 -2.447 0.472 3.354 -7.786 3.671 37.464 33 DD_G208C209:G237C238_DD D 208 ? D 238 ? D 209 ? D 237 ? 1 D C 9 1_555 D G 37 1_555 D C 10 1_555 D G 36 1_555 0.459 -1.694 3.741 2.917 2.312 23.619 -4.939 -0.036 3.590 5.605 -7.069 23.907 34 DD_C209C210:G236G237_DD D 209 ? D 237 ? D 210 ? D 236 ? 1 D C 10 1_555 D G 36 1_555 D G 11 1_555 D C 35 1_555 0.358 -1.778 3.037 -3.974 25.316 31.491 -4.706 -0.853 1.267 39.483 6.198 40.395 35 DD_C210G211:C235G236_DD D 210 ? D 236 ? D 211 ? D 235 ? 1 D G 11 1_555 D C 35 1_555 D U 12 1_555 D A 32 1_555 -2.821 -1.988 3.169 -2.870 1.010 85.091 -1.492 2.020 3.225 0.746 2.121 85.135 36 DD_G211U212:A232C235_DD D 211 ? D 235 ? D 212 ? D 232 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 "(3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A-TETRAHYDRO-4,9[1',2']-BENZENO-1H-BENZ[F]ISOINDOLE-1,3(2H)-DIONE" DAI 4 'MAGNESIUM ION' MG # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1YLS _pdbx_initial_refinement_model.details 'The Diels-Alder ribozyme structure from the Diels-Alder ribozyme-product complex, pdb entry 1YLS' #