data_1KSE # _entry.id 1KSE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 1KSE pdb_00001kse 10.2210/pdb1kse/pdb RCSB RCSB015293 ? ? WWPDB D_1000015293 ? ? # 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 2002-05-08 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 5 'Structure model' 1 4 2024-05-22 # _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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 5 'Structure model' 'Data collection' # 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' database_2 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_site 6 5 'Structure model' chem_comp_atom 7 5 'Structure model' chem_comp_bond # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_dist_value' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 19 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 20 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 21 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1KSE _pdbx_database_status.recvd_initial_deposition_date 2002-01-12 _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 'Tuma, J.' 1 'Connors, W.H.' 2 'Stitelman, D.H.' 3 'Richert, C.' 4 # _citation.id primary _citation.title 'On the effect of covalently appended quinolones on termini of DNA duplexes.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 124 _citation.page_first 4236 _citation.page_last 4246 _citation.year 2002 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11960452 _citation.pdbx_database_id_DOI 10.1021/ja0125117 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Tuma, J.' 1 ? primary 'Connors, W.H.' 2 ? primary 'Stitelman, D.H.' 3 ? primary 'Richert, C.' 4 ? # 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'-D(*(5AT)P*GP*CP*GP*CP*A)-3'" 1728.254 2 ? ? ? 'Quinolone-DNA hybrid' 2 non-polymer syn 'OXOLINIC ACID' 261.230 2 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(5AT)(DG)(DC)(DG)(DC)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TGCGCA _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'OXOLINIC ACID' _pdbx_entity_nonpoly.comp_id OXI # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 5AT n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 DA 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 'Custom synthesized by the authors' # 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 5AT 'DNA linking' n "5'-AMINO-5'-DEOXYTHYMIDINE" ? 'C10 H15 N3 O4' 241.244 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 OXI non-polymer . 'OXOLINIC ACID' ? 'C13 H11 N O5' 261.230 # 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 5AT 1 1 1 5AT T A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DA 6 6 6 DA A A . n B 1 1 5AT 1 1 1 5AT T B . n B 1 2 DG 2 2 2 DG G B . n B 1 3 DC 3 3 3 DC C B . n B 1 4 DG 4 4 4 DG G B . n B 1 5 DC 5 5 5 DC C B . n B 1 6 DA 6 6 6 DA A 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 2 OXI 1 0 1 OXI T A . D 2 OXI 1 0 1 OXI T B . # _exptl.entry_id 1KSE _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_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 ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _database_PDB_matrix.entry_id 1KSE _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 1KSE _struct.title 'Solution Structure of a quinolone-capped DNA duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1KSE _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, quinolone, Synthetic hybrid, disrupted terminal basepairs' # 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 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1KSE _struct_ref.pdbx_db_accession 1KSE _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1KSE A 1 ? 6 ? 1KSE 1 ? 6 ? 1 6 2 1 1KSE B 1 ? 6 ? 1KSE 1 ? 6 ? 1 6 # _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 # _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 # 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 none ? C OXI . C1 ? ? ? 1_555 A 5AT 1 "N5'" ? ? A OXI 0 A 5AT 1 1_555 ? ? ? ? ? ? ? 1.350 ? ? covale2 covale both ? A 5AT 1 "O3'" ? ? ? 1_555 A DG 2 P ? ? A 5AT 1 A DG 2 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale3 covale none ? D OXI . C1 ? ? ? 1_555 B 5AT 1 "N5'" ? ? B OXI 0 B 5AT 1 1_555 ? ? ? ? ? ? ? 1.357 ? ? covale4 covale both ? B 5AT 1 "O3'" ? ? ? 1_555 B DG 2 P ? ? B 5AT 1 B DG 2 1_555 ? ? ? ? ? ? ? 1.611 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A OXI 0 ? 4 'BINDING SITE FOR RESIDUE OXI A 0' AC2 Software B OXI 0 ? 4 'BINDING SITE FOR RESIDUE OXI B 0' # 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 4 5AT A 1 ? 5AT A 1 . ? 1_555 ? 2 AC1 4 DG A 2 ? DG A 2 . ? 1_555 ? 3 AC1 4 DC B 5 ? DC B 5 . ? 1_555 ? 4 AC1 4 DA B 6 ? DA B 6 . ? 1_555 ? 5 AC2 4 DC A 5 ? DC A 5 . ? 1_555 ? 6 AC2 4 DA A 6 ? DA A 6 . ? 1_555 ? 7 AC2 4 5AT B 1 ? 5AT B 1 . ? 1_555 ? 8 AC2 4 DG B 2 ? DG B 2 . ? 1_555 ? # 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 5AT 1 A 5AT 1 ? DT "5'-AMINO-5'-DEOXYTHYMIDINE" 2 B 5AT 1 B 5AT 1 ? DT "5'-AMINO-5'-DEOXYTHYMIDINE" # _pdbx_nmr_ensemble.entry_id 1KSE _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'closest to the average' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 'analyte buffer, salt, D2O' D2O 2 'analyte buffer, salt, H2O/D2O (85:15)' 'H2O/D2O (85:15)' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 283 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.ionic_strength '165 mM Phosphate buffer(KH2PO4/K2HPO4), NaCl at pH 7 (uncorrected for deuterium effect)' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY, DQF-COSY, TOCSY' 2 2 1 '2D NOESY' # _pdbx_nmr_refine.entry_id 1KSE _pdbx_nmr_refine.method 'Torsion-Angle Molecular Dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal CNS 1.0 'structure solution' Brunger 1 CNS 1.0 refinement Brunger 2 # 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 5AT "N5'" N N N 1 5AT N1 N N N 2 5AT C6 C N N 3 5AT C2 C N N 4 5AT O2 O N N 5 5AT N3 N N N 6 5AT C4 C N N 7 5AT O4 O N N 8 5AT C5 C N N 9 5AT C7 C N N 10 5AT "C2'" C N N 11 5AT "C5'" C N N 12 5AT "C4'" C N R 13 5AT "O4'" O N N 14 5AT "C1'" C N R 15 5AT "C3'" C N S 16 5AT "O3'" O N N 17 5AT HN51 H N N 18 5AT HN52 H N N 19 5AT H6 H N N 20 5AT H3 H N N 21 5AT H71 H N N 22 5AT H72 H N N 23 5AT H73 H N N 24 5AT "H2'" H N N 25 5AT "H2''" H N N 26 5AT "H5'" H N N 27 5AT "H5''" H N N 28 5AT "H4'" H N N 29 5AT "H1'" H N N 30 5AT "H3'" H N N 31 5AT "HO3'" H N N 32 DA OP3 O N N 33 DA P P N N 34 DA OP1 O N N 35 DA OP2 O N N 36 DA "O5'" O N N 37 DA "C5'" C N N 38 DA "C4'" C N R 39 DA "O4'" O N N 40 DA "C3'" C N S 41 DA "O3'" O N N 42 DA "C2'" C N N 43 DA "C1'" C N R 44 DA N9 N Y N 45 DA C8 C Y N 46 DA N7 N Y N 47 DA C5 C Y N 48 DA C6 C Y N 49 DA N6 N N N 50 DA N1 N Y N 51 DA C2 C Y N 52 DA N3 N Y N 53 DA C4 C Y N 54 DA HOP3 H N N 55 DA HOP2 H N N 56 DA "H5'" H N N 57 DA "H5''" H N N 58 DA "H4'" H N N 59 DA "H3'" H N N 60 DA "HO3'" H N N 61 DA "H2'" H N N 62 DA "H2''" H N N 63 DA "H1'" H N N 64 DA H8 H N N 65 DA H61 H N N 66 DA H62 H N N 67 DA H2 H N N 68 DC OP3 O N N 69 DC P P N N 70 DC OP1 O N N 71 DC OP2 O N N 72 DC "O5'" O N N 73 DC "C5'" C N N 74 DC "C4'" C N R 75 DC "O4'" O N N 76 DC "C3'" C N S 77 DC "O3'" O N N 78 DC "C2'" C N N 79 DC "C1'" C N R 80 DC N1 N N N 81 DC C2 C N N 82 DC O2 O N N 83 DC N3 N N N 84 DC C4 C N N 85 DC N4 N N N 86 DC C5 C N N 87 DC C6 C N N 88 DC HOP3 H N N 89 DC HOP2 H N N 90 DC "H5'" H N N 91 DC "H5''" H N N 92 DC "H4'" H N N 93 DC "H3'" H N N 94 DC "HO3'" H N N 95 DC "H2'" H N N 96 DC "H2''" H N N 97 DC "H1'" H N N 98 DC H41 H N N 99 DC H42 H N N 100 DC H5 H N N 101 DC H6 H N N 102 DG OP3 O N N 103 DG P P N N 104 DG OP1 O N N 105 DG OP2 O N N 106 DG "O5'" O N N 107 DG "C5'" C N N 108 DG "C4'" C N R 109 DG "O4'" O N N 110 DG "C3'" C N S 111 DG "O3'" O N N 112 DG "C2'" C N N 113 DG "C1'" C N R 114 DG N9 N Y N 115 DG C8 C Y N 116 DG N7 N Y N 117 DG C5 C Y N 118 DG C6 C N N 119 DG O6 O N N 120 DG N1 N N N 121 DG C2 C N N 122 DG N2 N N N 123 DG N3 N N N 124 DG C4 C Y N 125 DG HOP3 H N N 126 DG HOP2 H N N 127 DG "H5'" H N N 128 DG "H5''" H N N 129 DG "H4'" H N N 130 DG "H3'" H N N 131 DG "HO3'" H N N 132 DG "H2'" H N N 133 DG "H2''" H N N 134 DG "H1'" H N N 135 DG H8 H N N 136 DG H1 H N N 137 DG H21 H N N 138 DG H22 H N N 139 OXI C1 C N N 140 OXI O1 O N N 141 OXI C3 C Y N 142 OXI C2 C Y N 143 OXI N1 N Y N 144 OXI C4 C Y N 145 OXI O4 O N N 146 OXI C10 C Y N 147 OXI C9 C Y N 148 OXI C8 C Y N 149 OXI C5 C Y N 150 OXI C7 C Y N 151 OXI C6 C Y N 152 OXI O6 O N N 153 OXI O7 O N N 154 OXI C11 C N N 155 OXI C12 C N N 156 OXI C13 C N N 157 OXI O2 O N N 158 OXI H2 H N N 159 OXI H8 H N N 160 OXI H5 H N N 161 OXI H111 H N N 162 OXI H112 H N N 163 OXI H121 H N N 164 OXI H122 H N N 165 OXI H131 H N N 166 OXI H132 H N N 167 OXI H133 H N N 168 OXI HO2 H N N 169 # 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 5AT "N5'" "C5'" sing N N 1 5AT "N5'" HN51 sing N N 2 5AT "N5'" HN52 sing N N 3 5AT N1 C6 sing N N 4 5AT N1 C2 sing N N 5 5AT N1 "C1'" sing N N 6 5AT C6 C5 doub N N 7 5AT C6 H6 sing N N 8 5AT C2 O2 doub N N 9 5AT C2 N3 sing N N 10 5AT N3 C4 sing N N 11 5AT N3 H3 sing N N 12 5AT C4 O4 doub N N 13 5AT C4 C5 sing N N 14 5AT C5 C7 sing N N 15 5AT C7 H71 sing N N 16 5AT C7 H72 sing N N 17 5AT C7 H73 sing N N 18 5AT "C2'" "C1'" sing N N 19 5AT "C2'" "C3'" sing N N 20 5AT "C2'" "H2'" sing N N 21 5AT "C2'" "H2''" sing N N 22 5AT "C5'" "C4'" sing N N 23 5AT "C5'" "H5'" sing N N 24 5AT "C5'" "H5''" sing N N 25 5AT "C4'" "O4'" sing N N 26 5AT "C4'" "C3'" sing N N 27 5AT "C4'" "H4'" sing N N 28 5AT "O4'" "C1'" sing N N 29 5AT "C1'" "H1'" sing N N 30 5AT "C3'" "O3'" sing N N 31 5AT "C3'" "H3'" sing N N 32 5AT "O3'" "HO3'" sing N N 33 DA OP3 P sing N N 34 DA OP3 HOP3 sing N N 35 DA P OP1 doub N N 36 DA P OP2 sing N N 37 DA P "O5'" sing N N 38 DA OP2 HOP2 sing N N 39 DA "O5'" "C5'" sing N N 40 DA "C5'" "C4'" sing N N 41 DA "C5'" "H5'" sing N N 42 DA "C5'" "H5''" sing N N 43 DA "C4'" "O4'" sing N N 44 DA "C4'" "C3'" sing N N 45 DA "C4'" "H4'" sing N N 46 DA "O4'" "C1'" sing N N 47 DA "C3'" "O3'" sing N N 48 DA "C3'" "C2'" sing N N 49 DA "C3'" "H3'" sing N N 50 DA "O3'" "HO3'" sing N N 51 DA "C2'" "C1'" sing N N 52 DA "C2'" "H2'" sing N N 53 DA "C2'" "H2''" sing N N 54 DA "C1'" N9 sing N N 55 DA "C1'" "H1'" sing N N 56 DA N9 C8 sing Y N 57 DA N9 C4 sing Y N 58 DA C8 N7 doub Y N 59 DA C8 H8 sing N N 60 DA N7 C5 sing Y N 61 DA C5 C6 sing Y N 62 DA C5 C4 doub Y N 63 DA C6 N6 sing N N 64 DA C6 N1 doub Y N 65 DA N6 H61 sing N N 66 DA N6 H62 sing N N 67 DA N1 C2 sing Y N 68 DA C2 N3 doub Y N 69 DA C2 H2 sing N N 70 DA N3 C4 sing Y N 71 DC OP3 P sing N N 72 DC OP3 HOP3 sing N N 73 DC P OP1 doub N N 74 DC P OP2 sing N N 75 DC P "O5'" sing N N 76 DC OP2 HOP2 sing N N 77 DC "O5'" "C5'" sing N N 78 DC "C5'" "C4'" sing N N 79 DC "C5'" "H5'" sing N N 80 DC "C5'" "H5''" sing N N 81 DC "C4'" "O4'" sing N N 82 DC "C4'" "C3'" sing N N 83 DC "C4'" "H4'" sing N N 84 DC "O4'" "C1'" sing N N 85 DC "C3'" "O3'" sing N N 86 DC "C3'" "C2'" sing N N 87 DC "C3'" "H3'" sing N N 88 DC "O3'" "HO3'" sing N N 89 DC "C2'" "C1'" sing N N 90 DC "C2'" "H2'" sing N N 91 DC "C2'" "H2''" sing N N 92 DC "C1'" N1 sing N N 93 DC "C1'" "H1'" sing N N 94 DC N1 C2 sing N N 95 DC N1 C6 sing N N 96 DC C2 O2 doub N N 97 DC C2 N3 sing N N 98 DC N3 C4 doub N N 99 DC C4 N4 sing N N 100 DC C4 C5 sing N N 101 DC N4 H41 sing N N 102 DC N4 H42 sing N N 103 DC C5 C6 doub N N 104 DC C5 H5 sing N N 105 DC C6 H6 sing N N 106 DG OP3 P sing N N 107 DG OP3 HOP3 sing N N 108 DG P OP1 doub N N 109 DG P OP2 sing N N 110 DG P "O5'" sing N N 111 DG OP2 HOP2 sing N N 112 DG "O5'" "C5'" sing N N 113 DG "C5'" "C4'" sing N N 114 DG "C5'" "H5'" sing N N 115 DG "C5'" "H5''" sing N N 116 DG "C4'" "O4'" sing N N 117 DG "C4'" "C3'" sing N N 118 DG "C4'" "H4'" sing N N 119 DG "O4'" "C1'" sing N N 120 DG "C3'" "O3'" sing N N 121 DG "C3'" "C2'" sing N N 122 DG "C3'" "H3'" sing N N 123 DG "O3'" "HO3'" sing N N 124 DG "C2'" "C1'" sing N N 125 DG "C2'" "H2'" sing N N 126 DG "C2'" "H2''" sing N N 127 DG "C1'" N9 sing N N 128 DG "C1'" "H1'" sing N N 129 DG N9 C8 sing Y N 130 DG N9 C4 sing Y N 131 DG C8 N7 doub Y N 132 DG C8 H8 sing N N 133 DG N7 C5 sing Y N 134 DG C5 C6 sing N N 135 DG C5 C4 doub Y N 136 DG C6 O6 doub N N 137 DG C6 N1 sing N N 138 DG N1 C2 sing N N 139 DG N1 H1 sing N N 140 DG C2 N2 sing N N 141 DG C2 N3 doub N N 142 DG N2 H21 sing N N 143 DG N2 H22 sing N N 144 DG N3 C4 sing N N 145 OXI C1 O1 doub N N 146 OXI C1 C3 sing N N 147 OXI C1 O2 sing N N 148 OXI C3 C2 doub Y N 149 OXI C3 C4 sing Y N 150 OXI C2 N1 sing Y N 151 OXI C2 H2 sing N N 152 OXI N1 C9 sing Y N 153 OXI N1 C12 sing N N 154 OXI C4 O4 doub N N 155 OXI C4 C10 sing Y N 156 OXI C10 C9 doub Y N 157 OXI C10 C5 sing Y N 158 OXI C9 C8 sing Y N 159 OXI C8 C7 doub Y N 160 OXI C8 H8 sing N N 161 OXI C5 C6 doub Y N 162 OXI C5 H5 sing N N 163 OXI C7 C6 sing Y N 164 OXI C7 O7 sing N N 165 OXI C6 O6 sing N N 166 OXI O6 C11 sing N N 167 OXI O7 C11 sing N N 168 OXI C11 H111 sing N N 169 OXI C11 H112 sing N N 170 OXI C12 C13 sing N N 171 OXI C12 H121 sing N N 172 OXI C12 H122 sing N N 173 OXI C13 H131 sing N N 174 OXI C13 H132 sing N N 175 OXI C13 H133 sing N N 176 OXI O2 HO2 sing N N 177 # _ndb_struct_conf_na.entry_id 1KSE _ndb_struct_conf_na.feature 'b-form double 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 DG 2 1_555 B DC 5 1_555 -1.510 -0.658 0.378 -7.550 -7.786 -2.740 1 A_DG2:DC5_B A 2 ? B 5 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 -0.157 -0.184 0.390 -5.593 -5.073 -1.682 2 A_DC3:DG4_B A 3 ? B 4 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.001 -0.194 0.439 7.058 -2.748 -1.487 3 A_DG4:DC3_B A 4 ? B 3 ? 19 1 1 A DC 5 1_555 B DG 2 1_555 0.957 -0.427 -0.004 12.265 -12.002 -1.904 4 A_DC5:DG2_B A 5 ? B 2 ? 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 DG 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 0.100 0.112 3.238 -5.886 10.060 45.955 -0.673 -0.599 3.159 12.647 7.399 47.332 1 AA_DG2DC3:DG4DC5_BB A 2 ? B 5 ? A 3 ? B 4 ? 1 A DC 3 1_555 B DG 4 1_555 A DG 4 1_555 B DC 3 1_555 0.143 0.786 2.831 -0.282 6.009 32.743 0.484 -0.292 2.924 10.548 0.495 33.276 2 AA_DC3DG4:DC3DG4_BB A 3 ? B 4 ? A 4 ? B 3 ? 1 A DG 4 1_555 B DC 3 1_555 A DC 5 1_555 B DG 2 1_555 -0.306 0.432 3.233 9.785 13.276 40.853 -0.684 1.340 3.077 18.153 -13.379 43.925 3 AA_DG4DC5:DG2DC3_BB A 4 ? B 3 ? A 5 ? B 2 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DPX _pdbx_nmr_spectrometer.field_strength 600 # _atom_sites.entry_id 1KSE _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 1.000000 _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] 1.000000 _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 H N O P # loop_