data_1IK5 # _entry.id 1IK5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1IK5 pdb_00001ik5 10.2210/pdb1ik5/pdb NDB AR0033 ? ? RCSB RCSB013356 ? ? WWPDB D_1000013356 ? ? # 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 2001-11-09 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_conn_type 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' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.value' 10 4 'Structure model' '_struct_conn.conn_type_id' 11 4 'Structure model' '_struct_conn.id' 12 4 'Structure model' '_struct_conn.pdbx_dist_value' 13 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 14 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 15 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 16 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 17 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 19 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 21 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 22 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 23 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 24 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 25 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 28 4 'Structure model' '_struct_conn_type.id' 29 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 30 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 31 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1IK5 _pdbx_database_status.recvd_initial_deposition_date 2001-05-02 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name NDB _pdbx_database_related.db_id AR0029 _pdbx_database_related.details ;AR0029 is another crystal form containing spermine molecule ; _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Deng, J.' 1 'Xiong, Y.' 2 'Sudarsanakumar, C.' 3 'Shi, K.' 4 'Sundaralingam, M.' 5 # _citation.id primary _citation.title ;Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple. ; _citation.journal_abbrev RNA _citation.journal_volume 7 _citation.page_first 1425 _citation.page_last 1431 _citation.year 2001 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11680847 _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Deng, J.' 1 ? primary 'Xiong, Y.' 2 ? primary 'Sudarsanakumar, C.' 3 ? primary 'Shi, K.' 4 ? primary 'Sundaralingam, M.' 5 ? # 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 "5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P*C)-3'" 4503.547 1 ? ? ? 'potential hair pin fragment with highly conserved UUCG loop' 2 polymer syn "5'-R(*GP*GP*UP*AP*UP*UP*UP*UP*GP*GP*UP*AP*(CBR)P*C)-3'" 4504.531 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 water nat water 18.015 67 ? ? ? ? # 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 yes 'GGUAUUUCGGUA(CBR)C' GGUAUUUCGGUACC A ? 2 polyribonucleotide no yes 'GGUAUUUUGGUA(CBR)C' GGUAUUUUGGUACC B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'MAGNESIUM ION' MG 4 water HOH # 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 U n 1 4 A n 1 5 U n 1 6 U n 1 7 U n 1 8 C n 1 9 G n 1 10 G n 1 11 U n 1 12 A n 1 13 CBR n 1 14 C n 2 1 G n 2 2 G n 2 3 U n 2 4 A n 2 5 U n 2 6 U n 2 7 U n 2 8 U n 2 9 G n 2 10 G n 2 11 U n 2 12 A n 2 13 CBR n 2 14 C n # 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 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 U 3 3 3 U U A . n A 1 4 A 4 4 4 A A A . n A 1 5 U 5 5 5 U U 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 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n A 1 11 U 11 11 11 U U A . n A 1 12 A 12 12 12 A A A . n A 1 13 CBR 13 13 13 CBR B A . n A 1 14 C 14 14 14 C C A . n B 2 1 G 1 15 15 G G B . n B 2 2 G 2 16 16 G G B . n B 2 3 U 3 17 17 U U B . n B 2 4 A 4 18 18 A A B . n B 2 5 U 5 19 19 U U B . n B 2 6 U 6 20 20 U U B . n B 2 7 U 7 21 21 U U B . n B 2 8 U 8 22 22 U U B . n B 2 9 G 9 23 23 G G B . n B 2 10 G 10 24 24 G G B . n B 2 11 U 11 25 25 U U B . n B 2 12 A 12 26 26 A A B . n B 2 13 CBR 13 27 27 CBR B B . n B 2 14 C 14 28 28 C C B . 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 C 3 MG 1 98 98 MG MG2 A . D 3 MG 1 99 99 MG MG2 B . E 4 HOH 1 31 31 HOH HOH A . E 4 HOH 2 32 32 HOH HOH A . E 4 HOH 3 33 33 HOH HOH A . E 4 HOH 4 35 35 HOH HOH A . E 4 HOH 5 38 38 HOH HOH A . E 4 HOH 6 39 39 HOH HOH A . E 4 HOH 7 40 40 HOH HOH A . E 4 HOH 8 44 44 HOH HOH A . E 4 HOH 9 45 45 HOH HOH A . E 4 HOH 10 47 47 HOH HOH A . E 4 HOH 11 51 51 HOH HOH A . E 4 HOH 12 53 53 HOH HOH A . E 4 HOH 13 55 55 HOH HOH A . E 4 HOH 14 56 56 HOH HOH A . E 4 HOH 15 59 59 HOH HOH A . E 4 HOH 16 61 61 HOH HOH A . E 4 HOH 17 62 62 HOH HOH A . E 4 HOH 18 65 65 HOH HOH A . E 4 HOH 19 66 66 HOH HOH A . E 4 HOH 20 69 69 HOH HOH A . E 4 HOH 21 70 70 HOH HOH A . E 4 HOH 22 74 74 HOH HOH A . E 4 HOH 23 77 77 HOH HOH A . E 4 HOH 24 78 78 HOH HOH A . E 4 HOH 25 83 83 HOH HOH A . E 4 HOH 26 84 84 HOH HOH A . E 4 HOH 27 85 85 HOH HOH A . E 4 HOH 28 86 86 HOH HOH A . E 4 HOH 29 87 87 HOH HOH A . E 4 HOH 30 92 92 HOH HOH A . E 4 HOH 31 95 95 HOH HOH A . F 4 HOH 1 29 29 HOH HOH B . F 4 HOH 2 30 30 HOH HOH B . F 4 HOH 3 34 34 HOH HOH B . F 4 HOH 4 36 36 HOH HOH B . F 4 HOH 5 37 37 HOH HOH B . F 4 HOH 6 41 41 HOH HOH B . F 4 HOH 7 42 42 HOH HOH B . F 4 HOH 8 43 43 HOH HOH B . F 4 HOH 9 46 46 HOH HOH B . F 4 HOH 10 48 48 HOH HOH B . F 4 HOH 11 49 49 HOH HOH B . F 4 HOH 12 50 50 HOH HOH B . F 4 HOH 13 52 52 HOH HOH B . F 4 HOH 14 54 54 HOH HOH B . F 4 HOH 15 57 57 HOH HOH B . F 4 HOH 16 60 60 HOH HOH B . F 4 HOH 17 63 63 HOH HOH B . F 4 HOH 18 64 64 HOH HOH B . F 4 HOH 19 67 67 HOH HOH B . F 4 HOH 20 68 68 HOH HOH B . F 4 HOH 21 71 71 HOH HOH B . F 4 HOH 22 73 73 HOH HOH B . F 4 HOH 23 75 75 HOH HOH B . F 4 HOH 24 76 76 HOH HOH B . F 4 HOH 25 79 79 HOH HOH B . F 4 HOH 26 80 80 HOH HOH B . F 4 HOH 27 81 81 HOH HOH B . F 4 HOH 28 82 82 HOH HOH B . F 4 HOH 29 88 88 HOH HOH B . F 4 HOH 30 89 89 HOH HOH B . F 4 HOH 31 90 90 HOH HOH B . F 4 HOH 32 91 91 HOH HOH B . F 4 HOH 33 93 93 HOH HOH B . F 4 HOH 34 94 94 HOH HOH B . F 4 HOH 35 96 96 HOH HOH B . F 4 HOH 36 97 97 HOH HOH B . # 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 0 A U 7 ? C2 ? A U 7 C2 2 1 Y 0 A U 7 ? O2 ? A U 7 O2 3 1 Y 0 A U 7 ? C5 ? A U 7 C5 4 1 Y 0 B U 21 ? O2 ? B U 7 O2 5 1 Y 0 B U 21 ? C4 ? B U 7 C4 6 1 Y 0 B U 21 ? O4 ? B U 7 O4 7 1 Y 0 B U 21 ? C5 ? B U 7 C5 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement . ? 4 # _cell.entry_id 1IK5 _cell.length_a 60.04 _cell.length_b 29.53 _cell.length_c 52.44 _cell.angle_alpha 90 _cell.angle_beta 120.83 _cell.angle_gamma 90 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1IK5 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # _exptl.entry_id 1IK5 _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 45.26 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'cacodylate, magnesium chloride, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _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 cacodylate ? ? ? 1 2 1 MgCl2 ? ? ? 1 3 1 MPD ? ? ? 1 4 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 140 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date 2000-05-02 _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 graphite _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _refine.entry_id 1IK5 _refine.ls_number_reflns_obs 6948 _refine.ls_number_reflns_all 7463 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 10 _refine.ls_d_res_high 1.8 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.209 _refine.ls_R_factor_R_free 0.232 _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 683 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _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_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 ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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_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 584 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.number_atoms_solvent 67 _refine_hist.number_atoms_total 655 _refine_hist.d_res_high 1.8 _refine_hist.d_res_low 10 # _database_PDB_matrix.entry_id 1IK5 _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 1IK5 _struct.title 'Crystal Structure of a 14mer RNA Containing Double UU Bulges in Two Crystal Forms: A Novel U*(AU) Intramolecular Base Triple' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1IK5 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA duplex, UU-bulges, base triple, kink, 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 4 ? F N N 4 ? # 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 1IK5 1IK5 ? ? ? 2 2 PDB 1IK5 1IK5 ? ? ? # 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 1IK5 A 1 ? 14 ? 1IK5 1 ? 14 ? 1 14 2 2 1IK5 B 1 ? 14 ? 1IK5 15 ? 28 ? 15 28 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _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.pdbx_parent_biol_id ? _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 covale1 covale both ? A A 12 "O3'" ? ? ? 1_555 A CBR 13 P ? ? A A 12 A CBR 13 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale2 covale both ? A CBR 13 "O3'" ? ? ? 1_555 A C 14 P ? ? A CBR 13 A C 14 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale3 covale both ? B A 12 "O3'" ? ? ? 1_555 B CBR 13 P ? ? B A 26 B CBR 27 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale4 covale both ? B CBR 13 "O3'" ? ? ? 1_555 B C 14 P ? ? B CBR 27 B C 28 1_555 ? ? ? ? ? ? ? 1.607 ? ? metalc1 metalc ? ? E HOH . O ? ? ? 1_555 C MG . MG ? ? A HOH 32 A MG 98 1_555 ? ? ? ? ? ? ? 2.057 ? ? metalc2 metalc ? ? E HOH . O ? ? ? 1_555 C MG . MG ? ? A HOH 40 A MG 98 1_555 ? ? ? ? ? ? ? 2.201 ? ? metalc3 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 74 B MG 99 1_555 ? ? ? ? ? ? ? 2.139 ? ? metalc4 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 77 B MG 99 1_555 ? ? ? ? ? ? ? 2.274 ? ? metalc5 metalc ? ? E HOH . O ? ? ? 1_555 C MG . MG ? ? A HOH 78 A MG 98 1_555 ? ? ? ? ? ? ? 2.032 ? ? metalc6 metalc ? ? F HOH . O ? ? ? 1_555 D MG . MG ? ? B HOH 75 B MG 99 1_555 ? ? ? ? ? ? ? 2.094 ? ? metalc7 metalc ? ? F HOH . O ? ? ? 1_555 D MG . MG ? ? B HOH 76 B MG 99 1_555 ? ? ? ? ? ? ? 2.255 ? ? metalc8 metalc ? ? F HOH . O ? ? ? 1_555 D MG . MG ? ? B HOH 93 B MG 99 1_555 ? ? ? ? ? ? ? 2.600 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 14 N3 ? ? A G 1 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 14 O2 ? ? A G 1 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 14 N4 ? ? A G 1 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B CBR 13 N3 ? ? A G 2 B CBR 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B CBR 13 O2 ? ? A G 2 B CBR 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B CBR 13 N4 ? ? A G 2 B CBR 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 B A 12 N1 ? ? A U 3 B A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 B A 12 N6 ? ? A U 3 B A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 4 N6 ? ? ? 1_555 B U 6 O2 ? ? A A 4 B U 20 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog10 hydrog ? ? A A 4 N7 ? ? ? 1_555 B U 6 N3 ? ? A A 4 B U 20 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog11 hydrog ? ? A A 4 N1 ? ? ? 1_555 B U 11 N3 ? ? A A 4 B U 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 4 N6 ? ? ? 1_555 B U 11 O4 ? ? A A 4 B U 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 5 N3 ? ? ? 1_555 B G 10 O6 ? ? A U 5 B G 24 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A U 5 O2 ? ? ? 1_555 B G 10 N1 ? ? A U 5 B G 24 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog15 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 4 N7 ? ? A U 6 B A 18 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog16 hydrog ? ? A U 6 O2 ? ? ? 1_555 B A 4 N6 ? ? A U 6 B A 18 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog17 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 8 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 8 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 8 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 B U 8 O2 ? ? A G 9 B U 22 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog21 hydrog ? ? A G 10 N1 ? ? ? 1_555 B U 5 O2 ? ? A G 10 B U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A G 10 O6 ? ? ? 1_555 B U 5 N3 ? ? A G 10 B U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A U 11 N3 ? ? ? 1_555 B A 4 N1 ? ? A U 11 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 11 O4 ? ? ? 1_555 B A 4 N6 ? ? A U 11 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A A 12 N1 ? ? ? 1_555 B U 3 N3 ? ? A A 12 B U 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 12 N6 ? ? ? 1_555 B U 3 O4 ? ? A A 12 B U 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A CBR 13 N3 ? ? ? 1_555 B G 2 N1 ? ? A CBR 13 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A CBR 13 N4 ? ? ? 1_555 B G 2 O6 ? ? A CBR 13 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A CBR 13 O2 ? ? ? 1_555 B G 2 N2 ? ? A CBR 13 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 14 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 14 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 14 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 O ? E HOH . ? A HOH 32 ? 1_555 MG ? C MG . ? A MG 98 ? 1_555 O ? E HOH . ? A HOH 40 ? 1_555 94.8 ? 2 O ? E HOH . ? A HOH 32 ? 1_555 MG ? C MG . ? A MG 98 ? 1_555 O ? E HOH . ? A HOH 78 ? 1_555 86.5 ? 3 O ? E HOH . ? A HOH 40 ? 1_555 MG ? C MG . ? A MG 98 ? 1_555 O ? E HOH . ? A HOH 78 ? 1_555 100.5 ? 4 O ? E HOH . ? A HOH 74 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? E HOH . ? A HOH 77 ? 1_555 74.3 ? 5 O ? E HOH . ? A HOH 74 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 75 ? 1_555 93.5 ? 6 O ? E HOH . ? A HOH 77 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 75 ? 1_555 83.3 ? 7 O ? E HOH . ? A HOH 74 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 76 ? 1_555 113.7 ? 8 O ? E HOH . ? A HOH 77 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 76 ? 1_555 171.5 ? 9 O ? F HOH . ? B HOH 75 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 76 ? 1_555 93.0 ? 10 O ? E HOH . ? A HOH 74 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 93 ? 1_555 145.2 ? 11 O ? E HOH . ? A HOH 77 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 93 ? 1_555 71.6 ? 12 O ? F HOH . ? B HOH 75 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 93 ? 1_555 75.9 ? 13 O ? F HOH . ? B HOH 76 ? 1_555 MG ? D MG . ? B MG 99 ? 1_555 O ? F HOH . ? B HOH 93 ? 1_555 100.0 ? # 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 MG 98 ? 3 'BINDING SITE FOR RESIDUE MG A 98' AC2 Software B MG 99 ? 5 'BINDING SITE FOR RESIDUE MG B 99' # 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 3 HOH E . ? HOH A 32 . ? 1_555 ? 2 AC1 3 HOH E . ? HOH A 40 . ? 1_555 ? 3 AC1 3 HOH E . ? HOH A 78 . ? 1_555 ? 4 AC2 5 HOH E . ? HOH A 74 . ? 1_555 ? 5 AC2 5 HOH E . ? HOH A 77 . ? 1_555 ? 6 AC2 5 HOH F . ? HOH B 75 . ? 1_555 ? 7 AC2 5 HOH F . ? HOH B 76 . ? 1_555 ? 8 AC2 5 HOH F . ? HOH B 93 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "C3'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 U _pdbx_validate_rmsd_angle.auth_seq_id_1 7 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C2'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 U _pdbx_validate_rmsd_angle.auth_seq_id_2 7 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 U _pdbx_validate_rmsd_angle.auth_seq_id_3 7 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 107.03 _pdbx_validate_rmsd_angle.angle_target_value 101.50 _pdbx_validate_rmsd_angle.angle_deviation 5.53 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.80 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id U _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 20 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.112 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A CBR 13 A CBR 13 ? DC ? 2 B CBR 13 B CBR 27 ? DC ? # 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 CBR BR BR N N 73 CBR P P N N 74 CBR OP1 O N N 75 CBR OP2 O N N 76 CBR "O5'" O N N 77 CBR N1 N N N 78 CBR C6 C N N 79 CBR C2 C N N 80 CBR O2 O N N 81 CBR N3 N N N 82 CBR C4 C N N 83 CBR N4 N N N 84 CBR C5 C N N 85 CBR "C2'" C N N 86 CBR "C5'" C N N 87 CBR "C4'" C N R 88 CBR "O4'" O N N 89 CBR "C1'" C N R 90 CBR "C3'" C N S 91 CBR "O3'" O N N 92 CBR OP3 O N N 93 CBR HOP2 H N N 94 CBR H6 H N N 95 CBR H41 H N N 96 CBR H42 H N N 97 CBR "H2'" H N N 98 CBR "H2''" H N N 99 CBR "H5'" H N N 100 CBR "H5''" H N N 101 CBR "H4'" H N N 102 CBR "H1'" H N N 103 CBR "H3'" H N N 104 CBR "HO3'" H N N 105 CBR HOP3 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 MG MG MG N N 148 U OP3 O N N 149 U P P N N 150 U OP1 O N N 151 U OP2 O N N 152 U "O5'" O N N 153 U "C5'" C N N 154 U "C4'" C N R 155 U "O4'" O N N 156 U "C3'" C N S 157 U "O3'" O N N 158 U "C2'" C N R 159 U "O2'" O N N 160 U "C1'" C N R 161 U N1 N N N 162 U C2 C N N 163 U O2 O N N 164 U N3 N N N 165 U C4 C N N 166 U O4 O N N 167 U C5 C N N 168 U C6 C N N 169 U HOP3 H N N 170 U HOP2 H N N 171 U "H5'" H N N 172 U "H5''" H N N 173 U "H4'" H N N 174 U "H3'" H N N 175 U "HO3'" H N N 176 U "H2'" H N N 177 U "HO2'" H N N 178 U "H1'" H N N 179 U H3 H N N 180 U H5 H N N 181 U H6 H N N 182 # 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 CBR BR C5 sing N N 76 CBR P OP1 doub N N 77 CBR P OP2 sing N N 78 CBR P "O5'" sing N N 79 CBR P OP3 sing N N 80 CBR OP2 HOP2 sing N N 81 CBR "O5'" "C5'" sing N N 82 CBR N1 C6 sing N N 83 CBR N1 C2 sing N N 84 CBR N1 "C1'" sing N N 85 CBR C6 C5 doub N N 86 CBR C6 H6 sing N N 87 CBR C2 O2 doub N N 88 CBR C2 N3 sing N N 89 CBR N3 C4 doub N N 90 CBR C4 N4 sing N N 91 CBR C4 C5 sing N N 92 CBR N4 H41 sing N N 93 CBR N4 H42 sing N N 94 CBR "C2'" "C1'" sing N N 95 CBR "C2'" "C3'" sing N N 96 CBR "C2'" "H2'" sing N N 97 CBR "C2'" "H2''" sing N N 98 CBR "C5'" "C4'" sing N N 99 CBR "C5'" "H5'" sing N N 100 CBR "C5'" "H5''" sing N N 101 CBR "C4'" "O4'" sing N N 102 CBR "C4'" "C3'" sing N N 103 CBR "C4'" "H4'" sing N N 104 CBR "O4'" "C1'" sing N N 105 CBR "C1'" "H1'" sing N N 106 CBR "C3'" "O3'" sing N N 107 CBR "C3'" "H3'" sing N N 108 CBR "O3'" "HO3'" sing N N 109 CBR OP3 HOP3 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 U OP3 P sing N N 153 U OP3 HOP3 sing N N 154 U P OP1 doub N N 155 U P OP2 sing N N 156 U P "O5'" sing N N 157 U OP2 HOP2 sing N N 158 U "O5'" "C5'" sing N N 159 U "C5'" "C4'" sing N N 160 U "C5'" "H5'" sing N N 161 U "C5'" "H5''" sing N N 162 U "C4'" "O4'" sing N N 163 U "C4'" "C3'" sing N N 164 U "C4'" "H4'" sing N N 165 U "O4'" "C1'" sing N N 166 U "C3'" "O3'" sing N N 167 U "C3'" "C2'" sing N N 168 U "C3'" "H3'" sing N N 169 U "O3'" "HO3'" sing N N 170 U "C2'" "O2'" sing N N 171 U "C2'" "C1'" sing N N 172 U "C2'" "H2'" sing N N 173 U "O2'" "HO2'" sing N N 174 U "C1'" N1 sing N N 175 U "C1'" "H1'" sing N N 176 U N1 C2 sing N N 177 U N1 C6 sing N N 178 U C2 O2 doub N N 179 U C2 N3 sing N N 180 U N3 C4 sing N N 181 U N3 H3 sing N N 182 U C4 O4 doub N N 183 U C4 C5 sing N N 184 U C5 C6 doub N N 185 U C5 H5 sing N N 186 U C6 H6 sing N N 187 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1IK5 'a-form double helix' 1IK5 'bulge loop' 1IK5 '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 14 1_555 -0.505 -0.101 0.006 -4.698 -3.104 -1.458 1 A_G1:C28_B A 1 ? B 28 ? 19 1 1 A G 2 1_555 B CBR 13 1_555 -0.223 -0.192 -0.007 -5.312 -13.976 -0.212 2 A_G2:CBR27_B A 2 ? B 27 ? 19 1 1 A U 3 1_555 B A 12 1_555 0.156 -0.058 0.073 -1.428 -9.250 6.919 3 A_U3:A26_B A 3 ? B 26 ? 20 1 1 A A 4 1_555 B U 11 1_555 -0.006 -0.142 0.222 -0.838 -13.277 4.068 4 A_A4:U25_B A 4 ? B 25 ? 20 1 1 A U 5 1_555 B G 10 1_555 2.647 -0.654 0.151 7.830 -9.030 -2.127 5 A_U5:G24_B A 5 ? B 24 ? 28 ? 1 A C 8 1_555 B G 9 1_555 0.081 -0.156 -0.148 1.310 0.017 3.043 6 A_C8:G23_B A 8 ? B 23 ? 19 1 1 A G 9 1_555 B U 8 1_555 -0.179 -0.205 -0.242 -3.959 -3.998 0.302 7 A_G9:U22_B A 9 ? B 22 ? ? 1 1 A G 10 1_555 B U 5 1_555 -2.466 -0.486 0.206 -8.150 -3.730 0.270 8 A_G10:U19_B A 10 ? B 19 ? 28 ? 1 A U 11 1_555 B A 4 1_555 0.022 -0.095 0.051 2.234 -11.290 4.168 9 A_U11:A18_B A 11 ? B 18 ? 20 1 1 A A 12 1_555 B U 3 1_555 -0.250 0.000 0.317 2.676 -11.745 5.558 10 A_A12:U17_B A 12 ? B 17 ? 20 1 1 A CBR 13 1_555 B G 2 1_555 0.378 -0.101 -0.248 12.308 -14.448 0.281 11 A_CBR13:G16_B A 13 ? B 16 ? 19 1 1 A C 14 1_555 B G 1 1_555 0.472 -0.206 -0.173 8.308 -9.188 -2.145 12 A_C14:G15_B A 14 ? B 15 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 14 1_555 A G 2 1_555 B CBR 13 1_555 -0.416 -1.622 3.241 -1.703 7.690 33.506 -3.872 0.454 2.827 13.115 2.904 34.393 1 AA_G1G2:CBR27C28_BB A 1 ? B 28 ? A 2 ? B 27 ? 1 A G 2 1_555 B CBR 13 1_555 A U 3 1_555 B A 12 1_555 1.003 -1.763 3.177 1.790 3.210 30.839 -3.881 -1.547 3.034 6.010 -3.350 31.052 2 AA_G2U3:A26CBR27_BB A 2 ? B 27 ? A 3 ? B 26 ? 1 A U 3 1_555 B A 12 1_555 A A 4 1_555 B U 11 1_555 -0.665 -1.782 3.128 -2.036 8.745 27.807 -5.215 0.929 2.504 17.624 4.102 29.193 3 AA_U3A4:U25A26_BB A 3 ? B 26 ? A 4 ? B 25 ? 1 A A 4 1_555 B U 11 1_555 A U 5 1_555 B G 10 1_555 -0.429 -1.032 3.064 1.746 9.685 40.820 -2.350 0.763 2.740 13.647 -2.460 41.940 4 AA_A4U5:G24U25_BB A 4 ? B 25 ? A 5 ? B 24 ? 1 A U 5 1_555 B G 10 1_555 A C 8 1_555 B G 9 1_555 -1.859 -1.845 3.190 -2.173 8.904 38.726 -3.675 2.498 2.811 13.203 3.222 39.755 5 AA_U5C8:G23G24_BB A 5 ? B 24 ? A 8 ? B 23 ? 1 A C 8 1_555 B G 9 1_555 A G 9 1_555 B U 8 1_555 0.018 -2.445 3.436 0.741 5.533 21.906 -8.174 0.215 2.741 14.264 -1.910 22.597 6 AA_C8G9:U22G23_BB A 8 ? B 23 ? A 9 ? B 22 ? 1 A G 9 1_555 B U 8 1_555 A G 10 1_555 B U 5 1_555 2.049 -1.914 3.010 0.465 8.688 40.999 -3.465 -2.825 2.592 12.237 -0.656 41.873 7 AA_G9G10:U19U22_BB A 9 ? B 22 ? A 10 ? B 19 ? 1 A G 10 1_555 B U 5 1_555 A U 11 1_555 B A 4 1_555 0.129 -0.877 3.017 -0.149 9.712 38.184 -2.328 -0.208 2.722 14.560 0.223 39.355 8 AA_G10U11:A18U19_BB A 10 ? B 19 ? A 11 ? B 18 ? 1 A U 11 1_555 B A 4 1_555 A A 12 1_555 B U 3 1_555 0.179 -1.544 3.026 -2.064 11.941 30.354 -4.488 -0.620 2.258 21.747 3.759 32.631 9 AA_U11A12:U17A18_BB A 11 ? B 18 ? A 12 ? B 17 ? 1 A A 12 1_555 B U 3 1_555 A CBR 13 1_555 B G 2 1_555 -0.696 -1.568 3.062 1.598 2.044 33.163 -3.051 1.460 2.927 3.574 -2.795 33.262 10 AA_A12CBR13:G16U17_BB A 12 ? B 17 ? A 13 ? B 16 ? 1 A CBR 13 1_555 B G 2 1_555 A C 14 1_555 B G 1 1_555 0.196 -1.969 3.418 0.884 5.768 32.139 -4.496 -0.196 3.033 10.312 -1.580 32.651 11 AA_CBR13C14:G15G16_BB A 13 ? B 16 ? A 14 ? B 15 ? # _atom_sites.entry_id 1IK5 _atom_sites.fract_transf_matrix[1][1] 0.016656 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009941 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033864 _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] 0.022208 _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 BR C MG N O P # loop_