data_3K1V # _entry.id 3K1V # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3K1V pdb_00003k1v 10.2210/pdb3k1v/pdb NDB NA0185 ? ? RCSB RCSB055440 ? ? WWPDB D_1000055440 ? ? # 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 2009-10-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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 ? # 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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.value' 6 3 'Structure model' '_struct_conn.pdbx_dist_value' 7 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 13 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 17 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 18 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 19 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2009-10-06 _pdbx_database_PDB_obs_spr.pdb_id 3K1V _pdbx_database_PDB_obs_spr.replace_pdb_id 3FU4 _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3K1V _pdbx_database_status.recvd_initial_deposition_date 2009-09-28 _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 'Klein, D.J.' 1 'Edwards, T.E.' 2 ;Ferre-D'Amare, A.R. ; 3 # _citation.id primary _citation.title 'Cocrystal Structure of a Class I Preq1 Riboswitch Reveals a Pseudoknot Recognizing an Essential Hypermodified Nucleobase' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 16 _citation.page_first 343 _citation.page_last ? _citation.year 2009 _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 19234468 _citation.pdbx_database_id_DOI 10.1038/NSMB.1563 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Klein, D.J.' 1 ? primary 'Edwards, T.E.' 2 ? primary ;Ferre-D'Amare, A.R. ; 3 ? # 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 'PreQ1 riboswitch' 10835.524 1 ? ? ? ? 2 non-polymer syn 7-DEAZA-7-AMINOMETHYL-GUANINE 179.179 1 ? ? ? ? 3 non-polymer syn 'CALCIUM ION' 40.078 4 ? ? ? ? 4 water nat water 18.015 62 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code AGAGGUUCUAGCACAUCCCUCUAUAAAAAACUAA _entity_poly.pdbx_seq_one_letter_code_can AGAGGUUCUAGCACAUCCCUCUAUAAAAAACUAA _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 7-DEAZA-7-AMINOMETHYL-GUANINE PRF 3 'CALCIUM ION' CA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A n 1 2 G n 1 3 A n 1 4 G n 1 5 G n 1 6 U n 1 7 U n 1 8 C n 1 9 U n 1 10 A n 1 11 G n 1 12 C n 1 13 A n 1 14 C n 1 15 A n 1 16 U n 1 17 C n 1 18 C n 1 19 C n 1 20 U n 1 21 C n 1 22 U n 1 23 A n 1 24 U n 1 25 A n 1 26 A n 1 27 A n 1 28 A n 1 29 A n 1 30 A n 1 31 C n 1 32 U n 1 33 A n 1 34 A n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _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 'Chemically synthesized RNA corresponding to a mutant of the natural sequence from Bacillus subtilis' # 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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 PRF non-polymer . 7-DEAZA-7-AMINOMETHYL-GUANINE ? 'C7 H9 N5 O' 179.179 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 A 1 1 1 A A A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 U 7 7 7 U U A . n A 1 8 C 8 8 8 C C A . n A 1 9 U 9 9 9 U U A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 C 12 12 12 C C A . n A 1 13 A 13 13 ? ? ? A . n A 1 14 C 14 14 ? ? ? A . n A 1 15 A 15 15 ? ? ? A . n A 1 16 U 16 16 ? ? ? A . n A 1 17 C 17 17 17 C C A . n A 1 18 C 18 18 18 C C A . n A 1 19 C 19 19 19 C C A . n A 1 20 U 20 20 20 U U A . n A 1 21 C 21 21 21 C C A . n A 1 22 U 22 22 22 U U A . n A 1 23 A 23 23 23 A A A . n A 1 24 U 24 24 24 U U A . n A 1 25 A 25 25 25 A A A . n A 1 26 A 26 26 26 A A A . n A 1 27 A 27 27 27 A A A . n A 1 28 A 28 28 28 A A A . n A 1 29 A 29 29 29 A A A . n A 1 30 A 30 30 30 A A A . n A 1 31 C 31 31 31 C C A . n A 1 32 U 32 32 32 U U A . n A 1 33 A 33 33 33 A A A . n A 1 34 A 34 34 34 A A A . 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 B 2 PRF 1 301 301 PRF PRF A . C 3 CA 1 201 201 CA CA A . D 3 CA 1 203 203 CA CA A . E 3 CA 1 204 204 CA CA A . F 3 CA 1 205 205 CA CA A . G 4 HOH 1 102 102 HOH HOH A . G 4 HOH 2 103 103 HOH HOH A . G 4 HOH 3 104 104 HOH HOH A . G 4 HOH 4 105 105 HOH HOH A . G 4 HOH 5 106 106 HOH HOH A . G 4 HOH 6 108 108 HOH HOH A . G 4 HOH 7 109 109 HOH HOH A . G 4 HOH 8 110 110 HOH HOH A . G 4 HOH 9 111 111 HOH HOH A . G 4 HOH 10 112 112 HOH HOH A . G 4 HOH 11 113 113 HOH HOH A . G 4 HOH 12 114 114 HOH HOH A . G 4 HOH 13 115 115 HOH HOH A . G 4 HOH 14 116 116 HOH HOH A . G 4 HOH 15 117 117 HOH HOH A . G 4 HOH 16 118 118 HOH HOH A . G 4 HOH 17 119 119 HOH HOH A . G 4 HOH 18 121 121 HOH HOH A . G 4 HOH 19 122 122 HOH HOH A . G 4 HOH 20 123 123 HOH HOH A . G 4 HOH 21 124 124 HOH HOH A . G 4 HOH 22 125 125 HOH HOH A . G 4 HOH 23 126 126 HOH HOH A . G 4 HOH 24 127 127 HOH HOH A . G 4 HOH 25 129 129 HOH HOH A . G 4 HOH 26 130 130 HOH HOH A . G 4 HOH 27 131 131 HOH HOH A . G 4 HOH 28 132 132 HOH HOH A . G 4 HOH 29 133 133 HOH HOH A . G 4 HOH 30 134 134 HOH HOH A . G 4 HOH 31 135 135 HOH HOH A . G 4 HOH 32 136 136 HOH HOH A . G 4 HOH 33 137 137 HOH HOH A . G 4 HOH 34 138 138 HOH HOH A . G 4 HOH 35 139 139 HOH HOH A . G 4 HOH 36 140 140 HOH HOH A . G 4 HOH 37 141 141 HOH HOH A . G 4 HOH 38 142 142 HOH HOH A . G 4 HOH 39 146 146 HOH HOH A . G 4 HOH 40 147 147 HOH HOH A . G 4 HOH 41 148 148 HOH HOH A . G 4 HOH 42 149 149 HOH HOH A . G 4 HOH 43 151 151 HOH HOH A . G 4 HOH 44 152 152 HOH HOH A . G 4 HOH 45 153 153 HOH HOH A . G 4 HOH 46 155 155 HOH HOH A . G 4 HOH 47 156 156 HOH HOH A . G 4 HOH 48 157 157 HOH HOH A . G 4 HOH 49 158 158 HOH HOH A . G 4 HOH 50 159 159 HOH HOH A . G 4 HOH 51 160 160 HOH HOH A . G 4 HOH 52 161 161 HOH HOH A . G 4 HOH 53 162 162 HOH HOH A . G 4 HOH 54 163 163 HOH HOH A . G 4 HOH 55 164 164 HOH HOH A . G 4 HOH 56 165 165 HOH HOH A . G 4 HOH 57 166 166 HOH HOH A . G 4 HOH 58 167 167 HOH HOH A . G 4 HOH 59 168 168 HOH HOH A . G 4 HOH 60 169 169 HOH HOH A . G 4 HOH 61 170 170 HOH HOH A . G 4 HOH 62 202 202 HOH HOH A . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A C 12 ? "C5'" ? A C 12 "C5'" 2 1 Y 1 A C 12 ? "C4'" ? A C 12 "C4'" 3 1 Y 1 A C 12 ? "O4'" ? A C 12 "O4'" 4 1 Y 1 A C 12 ? "C3'" ? A C 12 "C3'" 5 1 Y 1 A C 12 ? "O3'" ? A C 12 "O3'" 6 1 Y 1 A C 12 ? "C2'" ? A C 12 "C2'" 7 1 Y 1 A C 12 ? "O2'" ? A C 12 "O2'" 8 1 Y 1 A C 12 ? "C1'" ? A C 12 "C1'" 9 1 Y 1 A C 12 ? N1 ? A C 12 N1 10 1 Y 1 A C 12 ? C2 ? A C 12 C2 11 1 Y 1 A C 12 ? O2 ? A C 12 O2 12 1 Y 1 A C 12 ? N3 ? A C 12 N3 13 1 Y 1 A C 12 ? C4 ? A C 12 C4 14 1 Y 1 A C 12 ? N4 ? A C 12 N4 15 1 Y 1 A C 12 ? C5 ? A C 12 C5 16 1 Y 1 A C 12 ? C6 ? A C 12 C6 17 1 Y 1 A C 17 ? P ? A C 17 P 18 1 Y 1 A C 17 ? OP1 ? A C 17 OP1 19 1 Y 1 A C 17 ? OP2 ? A C 17 OP2 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHASER phasing . ? 1 CNS refinement 1.2 ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 3K1V _cell.length_a 76.810 _cell.length_b 76.810 _cell.length_c 85.900 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3K1V _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3K1V _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.25 _exptl_crystal.density_percent_sol 45.34 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details '30% PEG 200, 50MM CACL2, 100MM HEPES-KOH PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 5.0.1' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 5.0.1 _diffrn_source.pdbx_wavelength 1.0 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 3K1V _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30.000 _reflns.d_resolution_high 2.200 _reflns.number_obs 4836 _reflns.number_all ? _reflns.percent_possible_obs 95.0 _reflns.pdbx_Rmerge_I_obs 0.08500 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.800 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.20 _reflns_shell.d_res_low 2.28 _reflns_shell.percent_possible_all 69.1 _reflns_shell.Rmerge_I_obs 0.41400 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 2.20 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3K1V _refine.ls_number_reflns_obs 4592 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.00 _refine.ls_d_res_high 2.20 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.230 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.230 _refine.ls_R_factor_R_free 0.269 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 483 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'ENGH & HUBER' _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 ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 3K1V _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs 0.32 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free 0.38 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _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 614 _refine_hist.pdbx_number_atoms_ligand 17 _refine_hist.number_atoms_solvent 62 _refine_hist.number_atoms_total 693 _refine_hist.d_res_high 2.20 _refine_hist.d_res_low 30.00 # 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 c_bond_d 0.004 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.32 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 3K1V _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 # _struct.entry_id 3K1V _struct.title 'Cocrystal structure of a mutant class-I preQ1 riboswitch' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3K1V _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA; APTAMER; RIBOSWITCH; QUEUOSINE; PREQ1, 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 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3K1V _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code AGAGGUUCUAGCACAUCCCUCUAUAAAAAACUAA _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession 3K1V _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3K1V _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 34 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3K1V _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 34 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 34 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # _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 # _struct_biol.id 1 _struct_biol.details ? # 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 ? ? A G 5 OP2 ? ? ? 1_555 D CA . CA ? ? A G 5 A CA 203 1_555 ? ? ? ? ? ? ? 2.347 ? ? metalc2 metalc ? ? A U 7 OP2 ? ? ? 1_555 E CA . CA ? ? A U 7 A CA 204 1_555 ? ? ? ? ? ? ? 2.273 ? ? metalc3 metalc ? ? A C 8 OP2 ? ? ? 1_555 C CA . CA ? ? A C 8 A CA 201 1_555 ? ? ? ? ? ? ? 2.289 ? ? metalc4 metalc ? ? A U 9 OP2 ? ? ? 1_555 E CA . CA ? ? A U 9 A CA 204 1_555 ? ? ? ? ? ? ? 2.170 ? ? metalc5 metalc ? ? G HOH . O ? ? ? 1_555 F CA . CA ? ? A HOH 102 A CA 205 1_555 ? ? ? ? ? ? ? 2.435 ? ? metalc6 metalc ? ? G HOH . O ? ? ? 1_555 F CA . CA ? ? A HOH 103 A CA 205 1_555 ? ? ? ? ? ? ? 2.778 ? ? metalc7 metalc ? ? G HOH . O ? ? ? 1_555 F CA . CA ? ? A HOH 104 A CA 205 1_555 ? ? ? ? ? ? ? 2.784 ? ? metalc8 metalc ? ? G HOH . O ? ? ? 1_555 F CA . CA ? ? A HOH 106 A CA 205 1_555 ? ? ? ? ? ? ? 2.694 ? ? metalc9 metalc ? ? G HOH . O ? ? ? 1_555 C CA . CA ? ? A HOH 108 A CA 201 1_555 ? ? ? ? ? ? ? 2.596 ? ? metalc10 metalc ? ? G HOH . O ? ? ? 1_555 C CA . CA ? ? A HOH 109 A CA 201 1_555 ? ? ? ? ? ? ? 2.605 ? ? metalc11 metalc ? ? G HOH . O ? ? ? 1_555 E CA . CA ? ? A HOH 110 A CA 204 1_555 ? ? ? ? ? ? ? 2.515 ? ? metalc12 metalc ? ? G HOH . O ? ? ? 1_555 E CA . CA ? ? A HOH 111 A CA 204 1_555 ? ? ? ? ? ? ? 2.397 ? ? metalc13 metalc ? ? G HOH . O ? ? ? 1_555 E CA . CA ? ? A HOH 112 A CA 204 1_555 ? ? ? ? ? ? ? 2.973 ? ? metalc14 metalc ? ? G HOH . O ? ? ? 1_555 E CA . CA ? ? A HOH 113 A CA 204 1_555 ? ? ? ? ? ? ? 2.466 ? ? metalc15 metalc ? ? G HOH . O ? ? ? 1_555 D CA . CA ? ? A HOH 122 A CA 203 1_555 ? ? ? ? ? ? ? 2.574 ? ? metalc16 metalc ? ? G HOH . O ? ? ? 1_555 E CA . CA ? ? A HOH 129 A CA 204 1_555 ? ? ? ? ? ? ? 2.532 ? ? metalc17 metalc ? ? G HOH . O ? ? ? 1_555 D CA . CA ? ? A HOH 134 A CA 203 1_555 ? ? ? ? ? ? ? 2.533 ? ? metalc18 metalc ? ? G HOH . O ? ? ? 1_555 D CA . CA ? ? A HOH 135 A CA 203 1_555 ? ? ? ? ? ? ? 2.772 ? ? metalc19 metalc ? ? G HOH . O ? ? ? 1_555 D CA . CA ? ? A HOH 137 A CA 203 1_555 ? ? ? ? ? ? ? 2.598 ? ? metalc20 metalc ? ? G HOH . O ? ? ? 1_555 D CA . CA ? ? A HOH 152 A CA 203 1_555 ? ? ? ? ? ? ? 2.879 ? ? hydrog1 hydrog ? ? A A 1 N1 ? ? ? 1_555 A U 22 N3 ? ? A A 1 A U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 1 N6 ? ? ? 1_555 A U 22 O4 ? ? A A 1 A U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 2 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 2 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 2 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 N2 ? ? ? 1_555 A U 24 O4 ? ? A G 2 A U 24 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 20 N3 ? ? A A 3 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 20 O4 ? ? A A 3 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 19 N3 ? ? A G 4 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 19 O2 ? ? A G 4 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 19 N4 ? ? A G 4 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 5 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 5 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 5 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 5 N2 ? ? ? 1_555 A A 28 N1 ? ? A G 5 A A 28 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog16 hydrog ? ? A G 5 N3 ? ? ? 1_555 A A 28 N6 ? ? A G 5 A A 28 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog17 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 29 N7 ? ? A U 6 A A 29 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog18 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 29 N6 ? ? A U 6 A A 29 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog19 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 30 N6 ? ? A U 6 A A 30 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog20 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 30 N7 ? ? A U 7 A A 30 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog21 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 30 N6 ? ? A U 7 A A 30 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog22 hydrog ? ? A C 8 N4 ? ? ? 1_555 A A 34 N1 ? ? A C 8 A A 34 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog23 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 33 N1 ? ? A U 9 A A 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 33 N6 ? ? A U 9 A A 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 32 N3 ? ? A A 10 A U 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 32 O4 ? ? A A 10 A U 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 31 N3 ? ? A G 11 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 11 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 31 N4 ? ? A G 11 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 18 O2 ? ? ? 1_555 A A 29 N6 ? ? A C 18 A A 29 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog31 hydrog ? ? A C 19 O2 ? ? ? 1_555 A A 27 N6 ? ? A C 19 A A 27 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog32 hydrog ? ? A U 20 O2 ? ? ? 1_555 A A 26 N6 ? ? A U 20 A A 26 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog33 hydrog ? ? A C 21 O2 ? ? ? 1_555 A A 25 N6 ? ? A C 21 A A 25 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP2 ? A G 5 ? A G 5 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 122 ? 1_555 115.2 ? 2 OP2 ? A G 5 ? A G 5 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 134 ? 1_555 91.4 ? 3 O ? G HOH . ? A HOH 122 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 134 ? 1_555 90.9 ? 4 OP2 ? A G 5 ? A G 5 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 135 ? 1_555 86.8 ? 5 O ? G HOH . ? A HOH 122 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 135 ? 1_555 139.1 ? 6 O ? G HOH . ? A HOH 134 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 135 ? 1_555 52.7 ? 7 OP2 ? A G 5 ? A G 5 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 137 ? 1_555 165.1 ? 8 O ? G HOH . ? A HOH 122 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 137 ? 1_555 79.7 ? 9 O ? G HOH . ? A HOH 134 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 137 ? 1_555 88.4 ? 10 O ? G HOH . ? A HOH 135 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 137 ? 1_555 81.2 ? 11 OP2 ? A G 5 ? A G 5 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 152 ? 1_555 82.9 ? 12 O ? G HOH . ? A HOH 122 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 152 ? 1_555 148.7 ? 13 O ? G HOH . ? A HOH 134 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 152 ? 1_555 115.0 ? 14 O ? G HOH . ? A HOH 135 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 152 ? 1_555 62.4 ? 15 O ? G HOH . ? A HOH 137 ? 1_555 CA ? D CA . ? A CA 203 ? 1_555 O ? G HOH . ? A HOH 152 ? 1_555 83.7 ? 16 OP2 ? A U 7 ? A U 7 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 OP2 ? A U 9 ? A U 9 ? 1_555 87.1 ? 17 OP2 ? A U 7 ? A U 7 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 110 ? 1_555 154.1 ? 18 OP2 ? A U 9 ? A U 9 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 110 ? 1_555 92.9 ? 19 OP2 ? A U 7 ? A U 7 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 111 ? 1_555 73.8 ? 20 OP2 ? A U 9 ? A U 9 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 111 ? 1_555 85.5 ? 21 O ? G HOH . ? A HOH 110 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 111 ? 1_555 80.3 ? 22 OP2 ? A U 7 ? A U 7 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 112 ? 1_555 133.0 ? 23 OP2 ? A U 9 ? A U 9 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 112 ? 1_555 107.0 ? 24 O ? G HOH . ? A HOH 110 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 112 ? 1_555 71.6 ? 25 O ? G HOH . ? A HOH 111 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 112 ? 1_555 149.6 ? 26 OP2 ? A U 7 ? A U 7 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 113 ? 1_555 86.1 ? 27 OP2 ? A U 9 ? A U 9 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 113 ? 1_555 166.9 ? 28 O ? G HOH . ? A HOH 110 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 113 ? 1_555 88.4 ? 29 O ? G HOH . ? A HOH 111 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 113 ? 1_555 81.9 ? 30 O ? G HOH . ? A HOH 112 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 113 ? 1_555 85.8 ? 31 OP2 ? A U 7 ? A U 7 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 129 ? 1_555 79.5 ? 32 OP2 ? A U 9 ? A U 9 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 129 ? 1_555 75.2 ? 33 O ? G HOH . ? A HOH 110 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 129 ? 1_555 125.6 ? 34 O ? G HOH . ? A HOH 111 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 129 ? 1_555 147.7 ? 35 O ? G HOH . ? A HOH 112 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 129 ? 1_555 62.5 ? 36 O ? G HOH . ? A HOH 113 ? 1_555 CA ? E CA . ? A CA 204 ? 1_555 O ? G HOH . ? A HOH 129 ? 1_555 114.4 ? 37 OP2 ? A C 8 ? A C 8 ? 1_555 CA ? C CA . ? A CA 201 ? 1_555 O ? G HOH . ? A HOH 108 ? 1_555 82.0 ? 38 OP2 ? A C 8 ? A C 8 ? 1_555 CA ? C CA . ? A CA 201 ? 1_555 O ? G HOH . ? A HOH 109 ? 1_555 89.3 ? 39 O ? G HOH . ? A HOH 108 ? 1_555 CA ? C CA . ? A CA 201 ? 1_555 O ? G HOH . ? A HOH 109 ? 1_555 153.0 ? 40 O ? G HOH . ? A HOH 102 ? 1_555 CA ? F CA . ? A CA 205 ? 1_555 O ? G HOH . ? A HOH 103 ? 1_555 92.6 ? 41 O ? G HOH . ? A HOH 102 ? 1_555 CA ? F CA . ? A CA 205 ? 1_555 O ? G HOH . ? A HOH 104 ? 1_555 83.9 ? 42 O ? G HOH . ? A HOH 103 ? 1_555 CA ? F CA . ? A CA 205 ? 1_555 O ? G HOH . ? A HOH 104 ? 1_555 81.6 ? 43 O ? G HOH . ? A HOH 102 ? 1_555 CA ? F CA . ? A CA 205 ? 1_555 O ? G HOH . ? A HOH 106 ? 1_555 87.1 ? 44 O ? G HOH . ? A HOH 103 ? 1_555 CA ? F CA . ? A CA 205 ? 1_555 O ? G HOH . ? A HOH 106 ? 1_555 179.2 ? 45 O ? G HOH . ? A HOH 104 ? 1_555 CA ? F CA . ? A CA 205 ? 1_555 O ? G HOH . ? A HOH 106 ? 1_555 99.2 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A PRF 301 ? 9 'BINDING SITE FOR RESIDUE PRF A 301' AC2 Software A CA 201 ? 7 'BINDING SITE FOR RESIDUE CA A 201' AC3 Software A CA 203 ? 6 'BINDING SITE FOR RESIDUE CA A 203' AC4 Software A CA 204 ? 7 'BINDING SITE FOR RESIDUE CA A 204' AC5 Software A CA 205 ? 10 'BINDING SITE FOR RESIDUE CA A 205' # 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 9 G A 5 ? G A 5 . ? 1_555 ? 2 AC1 9 U A 6 ? U A 6 . ? 1_555 ? 3 AC1 9 G A 11 ? G A 11 . ? 1_555 ? 4 AC1 9 C A 12 ? C A 12 . ? 1_555 ? 5 AC1 9 C A 17 ? C A 17 . ? 1_555 ? 6 AC1 9 C A 18 ? C A 18 . ? 1_555 ? 7 AC1 9 A A 30 ? A A 30 . ? 1_555 ? 8 AC1 9 C A 31 ? C A 31 . ? 1_555 ? 9 AC1 9 HOH G . ? HOH A 134 . ? 1_555 ? 10 AC2 7 C A 8 ? C A 8 . ? 1_555 ? 11 AC2 7 A A 33 ? A A 33 . ? 11_445 ? 12 AC2 7 HOH G . ? HOH A 108 . ? 1_555 ? 13 AC2 7 HOH G . ? HOH A 109 . ? 1_555 ? 14 AC2 7 HOH G . ? HOH A 155 . ? 1_555 ? 15 AC2 7 HOH G . ? HOH A 163 . ? 11_445 ? 16 AC2 7 HOH G . ? HOH A 202 . ? 11_445 ? 17 AC3 6 G A 5 ? G A 5 . ? 1_555 ? 18 AC3 6 HOH G . ? HOH A 122 . ? 1_555 ? 19 AC3 6 HOH G . ? HOH A 134 . ? 1_555 ? 20 AC3 6 HOH G . ? HOH A 135 . ? 1_555 ? 21 AC3 6 HOH G . ? HOH A 137 . ? 1_555 ? 22 AC3 6 HOH G . ? HOH A 152 . ? 1_555 ? 23 AC4 7 U A 7 ? U A 7 . ? 1_555 ? 24 AC4 7 U A 9 ? U A 9 . ? 1_555 ? 25 AC4 7 HOH G . ? HOH A 110 . ? 1_555 ? 26 AC4 7 HOH G . ? HOH A 111 . ? 1_555 ? 27 AC4 7 HOH G . ? HOH A 112 . ? 1_555 ? 28 AC4 7 HOH G . ? HOH A 113 . ? 1_555 ? 29 AC4 7 HOH G . ? HOH A 129 . ? 1_555 ? 30 AC5 10 HOH G . ? HOH A 102 . ? 11_445 ? 31 AC5 10 HOH G . ? HOH A 102 . ? 1_555 ? 32 AC5 10 HOH G . ? HOH A 103 . ? 1_555 ? 33 AC5 10 HOH G . ? HOH A 103 . ? 11_445 ? 34 AC5 10 HOH G . ? HOH A 104 . ? 1_555 ? 35 AC5 10 HOH G . ? HOH A 104 . ? 11_445 ? 36 AC5 10 HOH G . ? HOH A 105 . ? 11_445 ? 37 AC5 10 HOH G . ? HOH A 105 . ? 1_555 ? 38 AC5 10 HOH G . ? HOH A 106 . ? 1_555 ? 39 AC5 10 HOH G . ? HOH A 106 . ? 11_445 ? # 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 "C2'" A A 23 ? ? "C3'" A A 23 ? ? "O3'" A A 23 ? ? 125.03 113.70 11.33 1.60 N 2 1 "C2'" A A 29 ? ? "C3'" A A 29 ? ? "O3'" A A 29 ? ? 126.11 113.70 12.41 1.60 N # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A CA 205 ? F CA . 2 1 A HOH 103 ? G HOH . 3 1 A HOH 106 ? G HOH . 4 1 A HOH 167 ? G HOH . # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A A 13 ? A A 13 2 1 Y 1 A C 14 ? A C 14 3 1 Y 1 A A 15 ? A A 15 4 1 Y 1 A U 16 ? A U 16 # 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 CA CA CA N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 HOH O O N N 112 HOH H1 H N N 113 HOH H2 H N N 114 PRF N1 N N N 115 PRF C2 C N N 116 PRF N3 N N N 117 PRF C4 C Y N 118 PRF C5 C Y N 119 PRF C6 C N N 120 PRF O6 O N N 121 PRF C7 C Y N 122 PRF C10 C N N 123 PRF N11 N N N 124 PRF C8 C Y N 125 PRF N9 N Y N 126 PRF N2 N N N 127 PRF H91 H N N 128 PRF H101 H N N 129 PRF H102 H N N 130 PRF H111 H N N 131 PRF H112 H N N 132 PRF H81 H N N 133 PRF HN91 H N N 134 PRF HN21 H N N 135 PRF HN22 H N N 136 U OP3 O N N 137 U P P N N 138 U OP1 O N N 139 U OP2 O N N 140 U "O5'" O N N 141 U "C5'" C N N 142 U "C4'" C N R 143 U "O4'" O N N 144 U "C3'" C N S 145 U "O3'" O N N 146 U "C2'" C N R 147 U "O2'" O N N 148 U "C1'" C N R 149 U N1 N N N 150 U C2 C N N 151 U O2 O N N 152 U N3 N N N 153 U C4 C N N 154 U O4 O N N 155 U C5 C N N 156 U C6 C N N 157 U HOP3 H N N 158 U HOP2 H N N 159 U "H5'" H N N 160 U "H5''" H N N 161 U "H4'" H N N 162 U "H3'" H N N 163 U "HO3'" H N N 164 U "H2'" H N N 165 U "HO2'" H N N 166 U "H1'" H N N 167 U H3 H N N 168 U H5 H N N 169 U H6 H N N 170 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 PRF N1 C2 sing N N 118 PRF N1 C6 sing N N 119 PRF N1 H91 sing N N 120 PRF C2 N3 doub N N 121 PRF C2 N2 sing N N 122 PRF N3 C4 sing N N 123 PRF C4 C5 doub Y N 124 PRF C4 N9 sing Y N 125 PRF C5 C6 sing N N 126 PRF C5 C7 sing Y N 127 PRF C6 O6 doub N N 128 PRF C7 C10 sing N N 129 PRF C7 C8 doub Y N 130 PRF C10 N11 sing N N 131 PRF C10 H101 sing N N 132 PRF C10 H102 sing N N 133 PRF N11 H111 sing N N 134 PRF N11 H112 sing N N 135 PRF C8 N9 sing Y N 136 PRF C8 H81 sing N N 137 PRF N9 HN91 sing N N 138 PRF N2 HN21 sing N N 139 PRF N2 HN22 sing N N 140 U OP3 P sing N N 141 U OP3 HOP3 sing N N 142 U P OP1 doub N N 143 U P OP2 sing N N 144 U P "O5'" sing N N 145 U OP2 HOP2 sing N N 146 U "O5'" "C5'" sing N N 147 U "C5'" "C4'" sing N N 148 U "C5'" "H5'" sing N N 149 U "C5'" "H5''" sing N N 150 U "C4'" "O4'" sing N N 151 U "C4'" "C3'" sing N N 152 U "C4'" "H4'" sing N N 153 U "O4'" "C1'" sing N N 154 U "C3'" "O3'" sing N N 155 U "C3'" "C2'" sing N N 156 U "C3'" "H3'" sing N N 157 U "O3'" "HO3'" sing N N 158 U "C2'" "O2'" sing N N 159 U "C2'" "C1'" sing N N 160 U "C2'" "H2'" sing N N 161 U "O2'" "HO2'" sing N N 162 U "C1'" N1 sing N N 163 U "C1'" "H1'" sing N N 164 U N1 C2 sing N N 165 U N1 C6 sing N N 166 U C2 O2 doub N N 167 U C2 N3 sing N N 168 U N3 C4 sing N N 169 U N3 H3 sing N N 170 U C4 O4 doub N N 171 U C4 C5 sing N N 172 U C5 C6 doub N N 173 U C5 H5 sing N N 174 U C6 H6 sing N N 175 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3K1V 'double helix' 3K1V 'a-form double helix' 3K1V 'mismatched base pair' 3K1V '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 1 1_555 A U 22 1_555 -0.573 -0.298 0.218 -8.521 6.546 0.611 1 A_A1:U22_A A 1 ? A 22 ? 20 1 1 A G 2 1_555 A C 21 1_555 0.136 -0.040 -0.066 -9.300 -22.487 4.037 2 A_G2:C21_A A 2 ? A 21 ? 19 1 1 A A 3 1_555 A U 20 1_555 0.065 -0.111 0.232 1.514 -8.817 4.939 3 A_A3:U20_A A 3 ? A 20 ? 20 1 1 A G 4 1_555 A C 19 1_555 -0.123 -0.006 0.100 -1.407 -5.409 0.576 4 A_G4:C19_A A 4 ? A 19 ? 19 1 1 A G 5 1_555 A C 18 1_555 -0.093 -0.088 -0.144 4.988 -12.397 -1.005 5 A_G5:C18_A A 5 ? A 18 ? 19 1 1 A U 6 1_555 A A 29 1_555 -0.631 3.340 0.765 -15.419 -18.747 -71.567 6 A_U6:A29_A A 6 ? A 29 ? 23 3 1 A A 30 1_555 A U 7 1_555 0.716 -3.898 -0.224 2.566 3.609 72.383 7 A_A30:U7_A A 30 ? A 7 ? 23 3 1 A C 31 1_555 A G 11 1_555 0.090 0.074 -0.077 12.735 -26.757 -0.259 8 A_C31:G11_A A 31 ? A 11 ? 19 1 1 A U 32 1_555 A A 10 1_555 0.147 0.084 0.363 7.560 -14.660 3.474 9 A_U32:A10_A A 32 ? A 10 ? 20 1 1 A A 33 1_555 A U 9 1_555 -0.312 0.039 -0.015 -2.797 -24.349 6.578 10 A_A33:U9_A A 33 ? A 9 ? 20 1 1 A A 34 1_555 A C 8 1_555 2.934 0.480 -0.429 -5.559 -14.926 -6.983 11 A_A34:C8_A A 34 ? A 8 ? ? ? # 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 1 1_555 A U 22 1_555 A G 2 1_555 A C 21 1_555 0.602 -1.078 3.282 4.980 11.044 35.342 -3.104 -0.302 2.885 17.566 -7.921 37.298 1 AA_A1G2:C21U22_AA A 1 ? A 22 ? A 2 ? A 21 ? 1 A G 2 1_555 A C 21 1_555 A A 3 1_555 A U 20 1_555 0.098 -1.064 2.924 -1.889 -0.939 32.195 -1.764 -0.477 2.943 -1.691 3.401 32.263 2 AA_G2A3:U20C21_AA A 2 ? A 21 ? A 3 ? A 20 ? 1 A A 3 1_555 A U 20 1_555 A G 4 1_555 A C 19 1_555 0.129 -1.682 3.342 1.083 7.240 27.277 -5.063 -0.023 2.814 15.012 -2.246 28.225 3 AA_A3G4:C19U20_AA A 3 ? A 20 ? A 4 ? A 19 ? 1 A G 4 1_555 A C 19 1_555 A G 5 1_555 A C 18 1_555 -0.136 -1.613 3.257 4.695 0.034 33.563 -2.773 0.983 3.207 0.059 -8.081 33.881 4 AA_G4G5:C18C19_AA A 4 ? A 19 ? A 5 ? A 18 ? 1 A G 5 1_555 A C 18 1_555 A U 6 1_555 A A 29 1_555 -6.651 -1.015 1.458 13.746 7.278 19.115 -1.847 14.601 -2.843 18.455 -34.855 24.597 5 AA_G5U6:A29C18_AA A 5 ? A 18 ? A 6 ? A 29 ? 1 A U 6 1_555 A A 29 1_555 A A 30 1_555 A U 7 1_555 0.647 -0.402 3.230 6.853 3.805 31.685 -1.378 0.042 3.227 6.839 -12.316 32.616 6 AA_U6A30:U7A29_AA A 6 ? A 29 ? A 30 ? A 7 ? 1 A A 30 1_555 A U 7 1_555 A C 31 1_555 A G 11 1_555 0.881 -3.007 2.704 -7.660 11.090 80.927 -2.509 -0.820 2.273 8.491 5.865 81.851 7 AA_A30C31:G11U7_AA A 30 ? A 7 ? A 31 ? A 11 ? 1 A C 31 1_555 A G 11 1_555 A U 32 1_555 A A 10 1_555 0.040 -1.150 3.308 -5.916 9.839 35.242 -3.091 -0.832 2.853 15.743 9.465 37.008 8 AA_C31U32:A10G11_AA A 31 ? A 11 ? A 32 ? A 10 ? 1 A U 32 1_555 A A 10 1_555 A A 33 1_555 A U 9 1_555 -0.282 -1.375 3.120 0.935 18.403 32.863 -4.185 0.542 2.080 29.793 -1.514 37.552 9 AA_U32A33:U9A10_AA A 32 ? A 10 ? A 33 ? A 9 ? 1 A A 33 1_555 A U 9 1_555 A A 34 1_555 A C 8 1_555 -0.733 -0.638 3.297 3.694 6.961 49.071 -1.265 1.140 3.125 8.319 -4.414 49.661 10 AA_A33A34:C8U9_AA A 33 ? A 9 ? A 34 ? A 8 ? # _atom_sites.entry_id 3K1V _atom_sites.fract_transf_matrix[1][1] 0.013019 _atom_sites.fract_transf_matrix[1][2] 0.007517 _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] 0.015033 _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] 0.011641 _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 CA N O P # loop_