data_1KFO # _entry.id 1KFO # _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 1KFO pdb_00001kfo 10.2210/pdb1kfo/pdb NDB AR0039 ? ? RCSB RCSB014906 ? ? WWPDB D_1000014906 ? ? # 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 2001-12-07 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' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1KFO _pdbx_database_status.recvd_initial_deposition_date 2001-11-21 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Lima, S.' 1 'Hildenbrand, J.' 2 'Korostelev, A.' 3 'Hattman, S.' 4 'Li, H.' 5 # _citation.id primary _citation.title 'Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution.' _citation.journal_abbrev RNA _citation.journal_volume 8 _citation.page_first 924 _citation.page_last 932 _citation.year 2002 _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 12166647 _citation.pdbx_database_id_DOI 10.1017/S1355838202028893 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lima, S.' 1 ? primary 'Hildenbrand, J.' 2 ? primary 'Korostelev, A.' 3 ? primary 'Hattman, S.' 4 ? primary 'Li, H.' 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*AP*AP*UP*GP*CP*CP*UP*GP*CP*GP*AP*GP*CP*AP*(5BU)P*CP*CP*C)-3'" 6131.561 1 ? ? ? ? 2 water nat water 18.015 38 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GAAUGCCUGCGAGCA(5BU)CCC' _entity_poly.pdbx_seq_one_letter_code_can GAAUGCCUGCGAGCAUCCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 A n 1 3 A n 1 4 U n 1 5 G n 1 6 C n 1 7 C n 1 8 U n 1 9 G n 1 10 C n 1 11 G n 1 12 A n 1 13 G n 1 14 C n 1 15 A n 1 16 5BU n 1 17 C n 1 18 C n 1 19 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 A 2 2 2 A A A . n A 1 3 A 3 3 3 A A A . n A 1 4 U 4 4 4 U U A . n A 1 5 G 5 5 5 G G A . n A 1 6 C 6 6 6 C C A . n A 1 7 C 7 7 7 C C A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n A 1 10 C 10 10 10 C C A . n A 1 11 G 11 11 11 G G A . n A 1 12 A 12 12 12 A A A . n A 1 13 G 13 13 13 G G A . n A 1 14 C 14 14 14 C C A . n A 1 15 A 15 15 15 A A A . n A 1 16 5BU 16 16 16 5BU +U 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 # 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 HOH 1 20 1 HOH TIP A . B 2 HOH 2 21 2 HOH TIP A . B 2 HOH 3 22 3 HOH TIP A . B 2 HOH 4 23 4 HOH TIP A . B 2 HOH 5 24 5 HOH TIP A . B 2 HOH 6 25 6 HOH TIP A . B 2 HOH 7 26 7 HOH TIP A . B 2 HOH 8 27 8 HOH TIP A . B 2 HOH 9 28 9 HOH TIP A . B 2 HOH 10 29 10 HOH TIP A . B 2 HOH 11 30 11 HOH TIP A . B 2 HOH 12 31 12 HOH TIP A . B 2 HOH 13 32 13 HOH TIP A . B 2 HOH 14 33 14 HOH TIP A . B 2 HOH 15 34 15 HOH TIP A . B 2 HOH 16 35 16 HOH TIP A . B 2 HOH 17 36 17 HOH TIP A . B 2 HOH 18 37 18 HOH TIP A . B 2 HOH 19 38 19 HOH TIP A . B 2 HOH 20 39 20 HOH TIP A . B 2 HOH 21 40 21 HOH TIP A . B 2 HOH 22 41 22 HOH TIP A . B 2 HOH 23 42 23 HOH TIP A . B 2 HOH 24 43 24 HOH TIP A . B 2 HOH 25 44 25 HOH TIP A . B 2 HOH 26 45 26 HOH TIP A . B 2 HOH 27 46 27 HOH TIP A . B 2 HOH 28 47 28 HOH TIP A . B 2 HOH 29 48 29 HOH TIP A . B 2 HOH 30 49 30 HOH TIP A . B 2 HOH 31 50 31 HOH TIP A . B 2 HOH 32 51 32 HOH TIP A . B 2 HOH 33 52 33 HOH TIP A . B 2 HOH 34 53 34 HOH TIP A . B 2 HOH 35 54 35 HOH TIP A . B 2 HOH 36 55 36 HOH TIP A . B 2 HOH 37 56 37 HOH TIP A . B 2 HOH 38 57 38 HOH TIP A . # _software.name CNS _software.classification refinement _software.version 1.0 _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1KFO _cell.length_a 45.336 _cell.length_b 45.336 _cell.length_c 95.129 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KFO _symmetry.space_group_name_H-M 'P 63 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 # _exptl.entry_id 1KFO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.30 _exptl_crystal.density_percent_sol 46.55 _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _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 . _diffrn_radiation_wavelength.wt 1.0 # _reflns.entry_id 1KFO _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high ? _reflns.number_obs ? _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 16.5 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1KFO _refine.ls_number_reflns_obs 13798 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 635784.22 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.ls_d_res_low 16.69 _refine.ls_d_res_high 1.60 _refine.ls_percent_reflns_obs 95.4 _refine.ls_R_factor_obs 0.26 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.26 _refine.ls_R_factor_R_free 0.288 _refine.ls_R_factor_R_free_error 0.008 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.8 _refine.ls_number_reflns_R_free 1346 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 28.8 _refine.aniso_B[1][1] 2.94 _refine.aniso_B[2][2] 2.94 _refine.aniso_B[3][3] -5.88 _refine.aniso_B[1][2] 1.92 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.456314 _refine.solvent_model_param_bsol 42.3081 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _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.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1KFO _refine_analyze.Luzzati_coordinate_error_obs 0.25 _refine_analyze.Luzzati_sigma_a_obs 0.07 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.29 _refine_analyze.Luzzati_sigma_a_free 0.10 _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_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 400 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 439 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 16.69 # 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 0.008 ? ? ? '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 1.2 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 6.0 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.25 ? ? ? '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' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.60 _refine_ls_shell.d_res_low 1.70 _refine_ls_shell.number_reflns_R_work 1968 _refine_ls_shell.R_factor_R_work 0.286 _refine_ls_shell.percent_reflns_obs 90.8 _refine_ls_shell.R_factor_R_free 0.317 _refine_ls_shell.R_factor_R_free_error 0.022 _refine_ls_shell.percent_reflns_R_free 9.8 _refine_ls_shell.number_reflns_R_free 215 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 DNA-RNA_REP.PARAM ? 'X-RAY DIFFRACTION' 3 WATER_REP.PARAM ? 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1KFO _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 1KFO _struct.title 'CRYSTAL STRUCTURE OF AN RNA HELIX RECOGNIZED BY A ZINC-FINGER PROTEIN: AN 18 BASE PAIR DUPLEX AT 1.6 RESOLUTION' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1KFO _struct_keywords.pdbx_keywords RNA _struct_keywords.text 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1KFO _struct_ref.pdbx_db_accession 1KFO _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1KFO _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 19 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1KFO _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 19 _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 19 # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 8_555 x-y,-y,-z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 15 "O3'" ? ? ? 1_555 A 5BU 16 P ? ? A A 15 A 5BU 16 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale2 covale both ? A 5BU 16 "O3'" ? ? ? 1_555 A C 17 P ? ? A 5BU 16 A C 17 1_555 ? ? ? ? ? ? ? 1.611 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 1 A C 18 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 1 A C 18 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 1 A C 18 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N6 ? ? ? 1_555 A C 17 N3 ? ? A A 2 A C 17 7_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog5 hydrog ? ? A A 3 N1 ? ? ? 1_555 A 5BU 16 N3 ? ? A A 3 A 5BU 16 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N6 ? ? ? 1_555 A 5BU 16 O4 ? ? A A 3 A 5BU 16 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 15 N1 ? ? A U 4 A A 15 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 15 N6 ? ? A U 4 A A 15 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 5 A C 14 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 5 A C 14 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 5 A C 14 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 13 N1 ? ? A C 6 A G 13 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 13 O6 ? ? A C 6 A G 13 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 13 N2 ? ? A C 6 A G 13 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N3 ? ? ? 1_555 A A 12 N6 ? ? A C 7 A A 12 7_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog16 hydrog ? ? A U 8 N3 ? ? ? 1_555 A G 11 O6 ? ? A U 8 A G 11 7_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog17 hydrog ? ? A U 8 O2 ? ? ? 1_555 A G 11 N1 ? ? A U 8 A G 11 7_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog18 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 10 N3 ? ? A G 9 A C 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 10 O2 ? ? A G 9 A C 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 10 N4 ? ? A G 9 A C 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 9 N1 ? ? A C 10 A G 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 9 O6 ? ? A C 10 A G 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 9 N2 ? ? A C 10 A G 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 11 N1 ? ? ? 1_555 A U 8 O2 ? ? A G 11 A U 8 7_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog25 hydrog ? ? A G 11 O6 ? ? ? 1_555 A U 8 N3 ? ? A G 11 A U 8 7_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog26 hydrog ? ? A A 12 N6 ? ? ? 1_555 A C 7 N3 ? ? A A 12 A C 7 7_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog27 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 6 N3 ? ? A G 13 A C 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 6 O2 ? ? A G 13 A C 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 6 N4 ? ? A G 13 A C 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 5 N1 ? ? A C 14 A G 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 5 O6 ? ? A C 14 A G 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 5 N2 ? ? A C 14 A G 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A A 15 N1 ? ? ? 1_555 A U 4 N3 ? ? A A 15 A U 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A A 15 N6 ? ? ? 1_555 A U 4 O4 ? ? A A 15 A U 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A 5BU 16 N3 ? ? ? 1_555 A A 3 N1 ? ? A 5BU 16 A A 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A 5BU 16 O4 ? ? ? 1_555 A A 3 N6 ? ? A 5BU 16 A A 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 17 N3 ? ? ? 1_555 A A 2 N6 ? ? A C 17 A A 2 7_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog38 hydrog ? ? A C 18 N3 ? ? ? 1_555 A G 1 N1 ? ? A C 18 A G 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 18 N4 ? ? ? 1_555 A G 1 O6 ? ? A C 18 A G 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 18 O2 ? ? ? 1_555 A G 1 N2 ? ? A C 18 A G 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 "O2'" A A 3 ? ? 1_555 "C4'" A C 19 ? ? 5_555 0.89 2 1 "O2'" A A 3 ? ? 1_555 "C3'" A C 19 ? ? 5_555 1.05 3 1 "C4'" A A 3 ? ? 1_555 "O2'" A C 19 ? ? 5_555 1.20 4 1 "C3'" A A 3 ? ? 1_555 "O2'" A C 19 ? ? 5_555 1.36 5 1 "O3'" A A 3 ? ? 1_555 "O2'" A C 19 ? ? 5_555 1.44 6 1 "C2'" A A 3 ? ? 1_555 "O3'" A C 19 ? ? 5_555 1.55 7 1 "O3'" A A 3 ? ? 1_555 "C2'" A C 19 ? ? 5_555 1.62 8 1 "O2'" A A 3 ? ? 1_555 "O3'" A C 19 ? ? 5_555 1.64 9 1 "O2'" A A 3 ? ? 1_555 "C5'" A C 19 ? ? 5_555 1.74 10 1 "C2'" A A 3 ? ? 1_555 "C3'" A C 19 ? ? 5_555 1.90 11 1 "C2'" A A 3 ? ? 1_555 "C4'" A C 19 ? ? 5_555 1.91 12 1 "C5'" A A 3 ? ? 1_555 "O2'" A C 19 ? ? 5_555 1.92 13 1 "O3'" A A 3 ? ? 1_555 "O3'" A C 19 ? ? 5_555 1.99 14 1 "C3'" A A 3 ? ? 1_555 "O3'" A C 19 ? ? 5_555 2.04 15 1 "O3'" A A 3 ? ? 1_555 "C3'" A C 19 ? ? 5_555 2.11 16 1 "C3'" A A 3 ? ? 1_555 "C2'" A C 19 ? ? 5_555 2.13 17 1 "C5'" A U 4 ? ? 1_555 "O3'" A C 19 ? ? 5_555 2.19 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 P _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 C _pdbx_validate_rmsd_bond.auth_seq_id_1 19 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "O5'" _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 C _pdbx_validate_rmsd_bond.auth_seq_id_2 19 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.468 _pdbx_validate_rmsd_bond.bond_target_value 1.593 _pdbx_validate_rmsd_bond.bond_deviation -0.125 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.010 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A G 11 ? ? "C1'" A G 11 ? ? N9 A G 11 ? ? 112.84 108.50 4.34 0.70 N 2 1 "O5'" A C 19 ? ? P A C 19 ? ? OP2 A C 19 ? ? 88.43 105.70 -17.27 0.90 N # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 5BU _pdbx_struct_mod_residue.label_seq_id 16 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id 5BU _pdbx_struct_mod_residue.auth_seq_id 16 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id U _pdbx_struct_mod_residue.details "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # _pdbx_database_remark.id 99 _pdbx_database_remark.text ;Short contacts exhibited by residue 19 are due to the fact that residue 19 was not included in refinement and was left unrefined. ; # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 U OP3 O N N 148 U P P N N 149 U OP1 O N N 150 U OP2 O N N 151 U "O5'" O N N 152 U "C5'" C N N 153 U "C4'" C N R 154 U "O4'" O N N 155 U "C3'" C N S 156 U "O3'" O N N 157 U "C2'" C N R 158 U "O2'" O N N 159 U "C1'" C N R 160 U N1 N N N 161 U C2 C N N 162 U O2 O N N 163 U N3 N N N 164 U C4 C N N 165 U O4 O N N 166 U C5 C N N 167 U C6 C N N 168 U HOP3 H N N 169 U HOP2 H N N 170 U "H5'" H N N 171 U "H5''" H N N 172 U "H4'" H N N 173 U "H3'" H N N 174 U "HO3'" H N N 175 U "H2'" H N N 176 U "HO2'" H N N 177 U "H1'" H N N 178 U H3 H N N 179 U H5 H N N 180 U H6 H N N 181 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 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 1KFO 'double helix' 1KFO 'a-form double helix' 1KFO '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 A C 18 7_555 -0.475 -0.350 -0.181 -8.259 -10.553 -0.741 1 A_G1:C18_A A 1 ? A 18 ? 19 1 1 A A 2 1_555 A C 17 7_555 -2.067 -0.541 0.326 6.121 -15.481 11.318 2 A_A2:C17_A A 2 ? A 17 ? ? 1 1 A A 3 1_555 A 5BU 16 7_555 -0.007 -0.197 -0.021 1.367 -17.615 1.511 3 A_A3:5BU16_A A 3 ? A 16 ? 20 1 1 A U 4 1_555 A A 15 7_555 -0.048 -0.099 0.109 2.640 -14.016 6.252 4 A_U4:A15_A A 4 ? A 15 ? 20 1 1 A G 5 1_555 A C 14 7_555 -0.170 -0.194 -0.003 -0.543 -10.029 2.008 5 A_G5:C14_A A 5 ? A 14 ? 19 1 1 A C 6 1_555 A G 13 7_555 0.227 -0.215 -0.079 1.484 -12.541 -0.181 6 A_C6:G13_A A 6 ? A 13 ? 19 1 1 A C 7 1_555 A A 12 7_555 2.480 -0.508 0.194 -0.534 -8.005 7.567 7 A_C7:A12_A A 7 ? A 12 ? ? 1 1 A U 8 1_555 A G 11 7_555 2.339 -0.643 0.011 4.816 -13.947 -3.237 8 A_U8:G11_A A 8 ? A 11 ? 28 ? 1 A G 9 1_555 A C 10 7_555 -0.162 -0.165 0.047 -0.476 -6.572 -0.086 9 A_G9:C10_A A 9 ? A 10 ? 19 1 1 A C 10 1_555 A G 9 7_555 0.162 -0.165 0.047 0.476 -6.572 -0.086 10 A_C10:G9_A A 10 ? A 9 ? 19 1 1 A G 11 1_555 A U 8 7_555 -2.339 -0.643 0.011 -4.816 -13.947 -3.237 11 A_G11:U8_A A 11 ? A 8 ? 28 ? 1 A A 12 1_555 A C 7 7_555 -2.480 -0.508 0.194 0.534 -8.005 7.567 12 A_A12:C7_A A 12 ? A 7 ? ? 1 1 A G 13 1_555 A C 6 7_555 -0.227 -0.215 -0.079 -1.484 -12.541 -0.181 13 A_G13:C6_A A 13 ? A 6 ? 19 1 1 A C 14 1_555 A G 5 7_555 0.170 -0.194 -0.003 0.543 -10.029 2.008 14 A_C14:G5_A A 14 ? A 5 ? 19 1 1 A A 15 1_555 A U 4 7_555 0.048 -0.099 0.109 -2.640 -14.016 6.252 15 A_A15:U4_A A 15 ? A 4 ? 20 1 1 A 5BU 16 1_555 A A 3 7_555 0.007 -0.197 -0.021 -1.367 -17.615 1.511 16 A_5BU16:A3_A A 16 ? A 3 ? 20 1 1 A C 17 1_555 A A 2 7_555 2.067 -0.541 0.326 -6.121 -15.481 11.318 17 A_C17:A2_A A 17 ? A 2 ? ? 1 1 A C 18 1_555 A G 1 7_555 0.475 -0.350 -0.181 8.259 -10.553 -0.741 18 A_C18:G1_A A 18 ? A 1 ? 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 A C 18 7_555 A A 2 1_555 A C 17 7_555 0.223 -1.770 2.702 -6.421 9.611 28.556 -4.720 -1.344 1.925 18.553 12.394 30.761 1 AA_G1A2:C17C18_AA A 1 ? A 18 ? A 2 ? A 17 ? 1 A A 2 1_555 A C 17 7_555 A A 3 1_555 A 5BU 16 7_555 -0.358 -0.655 3.455 0.623 6.643 38.119 -1.837 0.619 3.293 10.076 -0.945 38.677 2 AA_A2A3:5BU16C17_AA A 2 ? A 17 ? A 3 ? A 16 ? 1 A A 3 1_555 A 5BU 16 7_555 A U 4 1_555 A A 15 7_555 0.463 -1.290 3.238 0.272 6.189 32.172 -3.305 -0.777 2.949 11.039 -0.485 32.748 3 AA_A3U4:A155BU16_AA A 3 ? A 16 ? A 4 ? A 15 ? 1 A U 4 1_555 A A 15 7_555 A G 5 1_555 A C 14 7_555 -0.371 -1.511 3.221 -0.612 10.245 31.133 -4.297 0.561 2.612 18.470 1.104 32.741 4 AA_U4G5:C14A15_AA A 4 ? A 15 ? A 5 ? A 14 ? 1 A G 5 1_555 A C 14 7_555 A C 6 1_555 A G 13 7_555 -0.310 -1.534 3.246 -0.757 6.530 32.761 -3.695 0.420 2.901 11.434 1.325 33.397 5 AA_G5C6:G13C14_AA A 5 ? A 14 ? A 6 ? A 13 ? 1 A C 6 1_555 A G 13 7_555 A C 7 1_555 A A 12 7_555 0.180 -1.295 3.396 -1.091 7.709 38.857 -2.815 -0.393 3.088 11.448 1.620 39.600 6 AA_C6C7:A12G13_AA A 6 ? A 13 ? A 7 ? A 12 ? 1 A C 7 1_555 A A 12 7_555 A U 8 1_555 A G 11 7_555 -0.284 -1.765 2.985 7.233 7.941 32.838 -4.014 1.424 2.392 13.601 -12.388 34.504 7 AA_C7U8:G11A12_AA A 7 ? A 12 ? A 8 ? A 11 ? 1 A U 8 1_555 A G 11 7_555 A G 9 1_555 A C 10 7_555 0.138 -2.611 3.243 0.706 9.674 16.824 -11.499 -0.136 1.528 30.033 -2.191 19.403 8 AA_U8G9:C10G11_AA A 8 ? A 11 ? A 9 ? A 10 ? 1 A G 9 1_555 A C 10 7_555 A C 10 1_555 A G 9 7_555 0.000 -2.302 3.267 0.000 2.246 32.517 -4.482 0.000 3.105 4.006 0.000 32.592 9 AA_G9C10:G9C10_AA A 9 ? A 10 ? A 10 ? A 9 ? 1 A C 10 1_555 A G 9 7_555 A G 11 1_555 A U 8 7_555 -0.138 -2.611 3.243 -0.706 9.674 16.824 -11.499 0.136 1.528 30.034 2.191 19.403 10 AA_C10G11:U8G9_AA A 10 ? A 9 ? A 11 ? A 8 ? 1 A G 11 1_555 A U 8 7_555 A A 12 1_555 A C 7 7_555 0.284 -1.765 2.985 -7.233 7.941 32.838 -4.014 -1.424 2.392 13.601 12.388 34.504 11 AA_G11A12:C7U8_AA A 11 ? A 8 ? A 12 ? A 7 ? 1 A A 12 1_555 A C 7 7_555 A G 13 1_555 A C 6 7_555 -0.180 -1.295 3.396 1.091 7.709 38.857 -2.815 0.393 3.088 11.448 -1.620 39.600 12 AA_A12G13:C6C7_AA A 12 ? A 7 ? A 13 ? A 6 ? 1 A G 13 1_555 A C 6 7_555 A C 14 1_555 A G 5 7_555 0.310 -1.534 3.246 0.757 6.530 32.761 -3.695 -0.420 2.901 11.434 -1.325 33.397 13 AA_G13C14:G5C6_AA A 13 ? A 6 ? A 14 ? A 5 ? 1 A C 14 1_555 A G 5 7_555 A A 15 1_555 A U 4 7_555 0.371 -1.511 3.221 0.612 10.245 31.133 -4.297 -0.561 2.612 18.470 -1.104 32.741 14 AA_C14A15:U4G5_AA A 14 ? A 5 ? A 15 ? A 4 ? 1 A A 15 1_555 A U 4 7_555 A 5BU 16 1_555 A A 3 7_555 -0.463 -1.290 3.238 -0.272 6.189 32.172 -3.305 0.777 2.949 11.039 0.485 32.748 15 AA_A155BU16:A3U4_AA A 15 ? A 4 ? A 16 ? A 3 ? 1 A 5BU 16 1_555 A A 3 7_555 A C 17 1_555 A A 2 7_555 0.358 -0.655 3.455 -0.623 6.643 38.119 -1.837 -0.619 3.293 10.076 0.945 38.677 16 AA_5BU16C17:A2A3_AA A 16 ? A 3 ? A 17 ? A 2 ? 1 A C 17 1_555 A A 2 7_555 A C 18 1_555 A G 1 7_555 -0.223 -1.770 2.702 6.421 9.611 28.556 -4.720 1.344 1.925 18.553 -12.394 30.761 17 AA_C17C18:G1A2_AA A 17 ? A 2 ? A 18 ? A 1 ? # _atom_sites.entry_id 1KFO _atom_sites.fract_transf_matrix[1][1] 0.022058 _atom_sites.fract_transf_matrix[1][2] 0.012735 _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] 0.025470 _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] 0.010512 _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 N O P # loop_