data_1KXS # _entry.id 1KXS # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1KXS pdb_00001kxs 10.2210/pdb1kxs/pdb RCSB RCSB015447 ? ? WWPDB D_1000015447 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1KXS _pdbx_database_status.recvd_initial_deposition_date 2002-02-01 _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 'Boulard, Y.' 1 'Fazakerley, G.V.' 2 'Sowers, L.C.' 3 # _citation.id primary _citation.title ;The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 30 _citation.page_first 1371 _citation.page_last 1378 _citation.year 2002 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11884635 _citation.pdbx_database_id_DOI 10.1093/nar/30.6.1371 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Boulard, Y.' 1 ? primary 'Fazakerley, G.V.' 2 ? primary 'Sowers, L.C.' 3 ? # _cell.entry_id 1KXS _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KXS _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # 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(*GP*CP*AP*AP*GP*TP*CP*(HEU)P*AP*AP*AP*AP*CP*G)-3'" 4327.857 1 ? ? ? ? 2 polymer syn "5'-D(*CP*GP*TP*TP*TP*TP*AP*GP*AP*CP*TP*TP*GP*C)-3'" 4261.775 1 ? ? ? ? # 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 polydeoxyribonucleotide no yes '(DG)(DC)(DA)(DA)(DG)(DT)(DC)(HEU)(DA)(DA)(DA)(DA)(DC)(DG)' GCAAGTCUAAAACG A ? 2 polydeoxyribonucleotide no no '(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DG)(DA)(DC)(DT)(DT)(DG)(DC)' CGTTTTAGACTTGC B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DA n 1 4 DA n 1 5 DG n 1 6 DT n 1 7 DC n 1 8 HEU n 1 9 DA n 1 10 DA n 1 11 DA n 1 12 DA n 1 13 DC n 1 14 DG n 2 1 DC n 2 2 DG n 2 3 DT n 2 4 DT n 2 5 DT n 2 6 DT n 2 7 DA n 2 8 DG n 2 9 DA n 2 10 DC n 2 11 DT n 2 12 DT n 2 13 DG n 2 14 DC n # 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 1KXS 1KXS ? ? ? 2 2 PDB 1KXS 1KXS ? ? ? # 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 1KXS A 1 ? 14 ? 1KXS 1 ? 14 ? 1 14 2 2 1KXS B 1 ? 14 ? 1KXS 15 ? 28 ? 15 28 # 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 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HEU 'DNA linking' n "3-(2-HYDROXYETHYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C11 H17 N2 O9 P' 352.234 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 1 DQF-COSY 1 3 1 TOCSY 1 4 1 DQ 1 5 1 'HSQC 1H-31P' 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 293 _pdbx_nmr_exptl_sample_conditions.pressure AMBIENT _pdbx_nmr_exptl_sample_conditions.pH 6.7 _pdbx_nmr_exptl_sample_conditions.ionic_strength '10 mM PHOSPHATE BUFFER, 5 NACL, 0.2 mM EDTA' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.5 MM' _pdbx_nmr_sample_details.solvent_system ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 AVANCE Bruker 600 ? 2 AVANCE Bruker 500 ? # _pdbx_nmr_refine.entry_id 1KXS _pdbx_nmr_refine.method 'RESTRAINED MOLECULAR DYNA SIMULATIONS' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1KXS _pdbx_nmr_details.text ;THE STRUCTURES WERE DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS. THE BEST REPRESENTATIVE STRUCTURES ARE PRESENTED, MODELS 1 AND 2. ; # _pdbx_nmr_ensemble.entry_id 1KXS _pdbx_nmr_ensemble.conformers_calculated_total_number 256 _pdbx_nmr_ensemble.conformers_submitted_total_number 2 _pdbx_nmr_ensemble.conformer_selection_criteria 'Fit with NMR constraints and energy' _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_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'data analysis' XwinNMR 2.5 ? 1 refinement Amber ? KOLLMAN 2 refinement 'MORCAD AND OCL' ? LEBRET 3 refinement MOLMOL 2.6 KORADI 4 # _exptl.entry_id 1KXS _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.density_Matthews ? _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.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _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 # _struct.entry_id 1KXS _struct.title ;NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1KXS _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'MODIFIED BASE, MUTAGENESIS, DEOXYRIBONUCLEIC ACID, DNA' # 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_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 DC 7 "O3'" ? ? ? 1_555 A HEU 8 P ? ? A DC 7 A HEU 8 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale2 covale both ? A HEU 8 "O3'" ? ? ? 1_555 A DA 9 P ? ? A HEU 8 A DA 9 1_555 ? ? ? ? ? ? ? 1.618 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 14 N3 ? ? A DG 1 B DC 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 14 O2 ? ? A DG 1 B DC 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 14 N4 ? ? A DG 1 B DC 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DT 12 O4 ? ? A DC 2 B DT 26 1_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog5 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 13 N1 ? ? A DC 2 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 13 O6 ? ? A DC 2 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 13 N2 ? ? A DC 2 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 11 O4 ? ? A DA 3 B DT 25 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog9 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 12 N3 ? ? A DA 3 B DT 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 12 O4 ? ? A DA 3 B DT 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 11 N3 ? ? A DA 4 B DT 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 11 O4 ? ? A DA 4 B DT 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 5 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 5 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 5 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 9 N1 ? ? A DT 6 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 9 N6 ? ? A DT 6 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 8 N1 ? ? A DC 7 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 8 O6 ? ? A DC 7 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 8 N2 ? ? A DC 7 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 9 B DT 19 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog22 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 9 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 9 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 10 B DT 18 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog25 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 10 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 10 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DA 11 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 11 B DT 17 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog28 hydrog ? ? A DA 11 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 11 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DA 11 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 11 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 12 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 12 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 13 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 13 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 13 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DG 14 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 14 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DG 14 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 14 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DG 14 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 14 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1KXS _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1KXS _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_ _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 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 HEU 8 8 8 HEU HEU A . n A 1 9 DA 9 9 9 DA A A . n A 1 10 DA 10 10 10 DA A A . n A 1 11 DA 11 11 11 DA A A . n A 1 12 DA 12 12 12 DA A A . n A 1 13 DC 13 13 13 DC C A . n A 1 14 DG 14 14 14 DG G A . n B 2 1 DC 1 15 15 DC C B . n B 2 2 DG 2 16 16 DG G B . n B 2 3 DT 3 17 17 DT T B . n B 2 4 DT 4 18 18 DT T B . n B 2 5 DT 5 19 19 DT T B . n B 2 6 DT 6 20 20 DT T B . n B 2 7 DA 7 21 21 DA A B . n B 2 8 DG 8 22 22 DG G B . n B 2 9 DA 9 23 23 DA A B . n B 2 10 DC 10 24 24 DC C B . n B 2 11 DT 11 25 25 DT T B . n B 2 12 DT 12 26 26 DT T B . n B 2 13 DG 13 27 27 DG G B . n B 2 14 DC 14 28 28 DC C B . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id HEU _pdbx_struct_mod_residue.label_seq_id 8 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id HEU _pdbx_struct_mod_residue.auth_seq_id 8 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DU _pdbx_struct_mod_residue.details ? # _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 # _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 # 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 2002-03-06 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' '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' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_nmr_spectrometer 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 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' '_pdbx_nmr_software.name' 4 4 'Structure model' '_pdbx_nmr_spectrometer.model' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 110.17 108.30 1.87 0.30 N 2 1 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 110.42 108.30 2.12 0.30 N 3 1 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.14 108.30 1.84 0.30 N 4 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 110.96 108.30 2.66 0.30 N 5 1 "O4'" B DA 21 ? ? "C1'" B DA 21 ? ? N9 B DA 21 ? ? 110.94 108.30 2.64 0.30 N 6 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 110.65 108.30 2.35 0.30 N 7 1 "O4'" B DT 25 ? ? "C1'" B DT 25 ? ? N1 B DT 25 ? ? 110.39 108.30 2.09 0.30 N 8 1 "O4'" B DT 26 ? ? "C1'" B DT 26 ? ? N1 B DT 26 ? ? 110.50 108.30 2.20 0.30 N 9 2 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 110.44 108.30 2.14 0.30 N 10 2 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 110.18 108.30 1.88 0.30 N 11 2 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 110.21 108.30 1.91 0.30 N 12 2 C6 B DT 20 ? ? C5 B DT 20 ? ? C7 B DT 20 ? ? 119.26 122.90 -3.64 0.60 N 13 2 "O4'" B DT 25 ? ? "C1'" B DT 25 ? ? N1 B DT 25 ? ? 110.38 108.30 2.08 0.30 N 14 2 "O4'" B DT 26 ? ? "C1'" B DT 26 ? ? N1 B DT 26 ? ? 110.49 108.30 2.19 0.30 N 15 2 "O4'" B DC 28 ? ? "C1'" B DC 28 ? ? N1 B DC 28 ? ? 110.15 108.30 1.85 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DA B 21 ? ? 0.063 'SIDE CHAIN' 2 1 DG B 27 ? ? 0.069 'SIDE CHAIN' 3 2 DT A 6 ? ? 0.061 'SIDE CHAIN' 4 2 DA B 23 ? ? 0.053 'SIDE CHAIN' 5 2 DG B 27 ? ? 0.066 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1KXS 'double helix' 1KXS 'b-form double helix' 1KXS 'mismatched base pair' 1KXS 'triple 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 1 1_555 B DC 14 1_555 0.099 -0.189 0.815 -7.611 -11.667 -5.991 1 A_DG1:DC28_B A 1 ? B 28 ? 19 1 1 A DC 2 1_555 B DG 13 1_555 -0.197 -0.084 0.942 -18.785 -2.568 -4.805 2 A_DC2:DG27_B A 2 ? B 27 ? 19 1 1 A DA 3 1_555 B DT 12 1_555 -0.072 -0.119 0.521 1.055 -14.613 -8.704 3 A_DA3:DT26_B A 3 ? B 26 ? 20 1 1 A DA 4 1_555 B DT 11 1_555 0.157 -0.118 0.672 3.672 -18.232 -12.029 4 A_DA4:DT25_B A 4 ? B 25 ? 20 1 1 A DG 5 1_555 B DC 10 1_555 -0.162 -0.196 0.809 3.312 -12.357 -7.165 5 A_DG5:DC24_B A 5 ? B 24 ? 19 1 1 A DT 6 1_555 B DA 9 1_555 0.005 -0.077 0.592 -2.770 -11.622 -8.825 6 A_DT6:DA23_B A 6 ? B 23 ? 20 1 1 A DC 7 1_555 B DG 8 1_555 0.052 -0.072 0.388 4.932 -12.532 -6.443 7 A_DC7:DG22_B A 7 ? B 22 ? 19 1 1 A DA 9 1_555 B DT 6 1_555 0.131 -0.127 0.880 3.375 -13.385 -13.974 8 A_DA9:DT20_B A 9 ? B 20 ? 20 1 1 A DA 10 1_555 B DT 5 1_555 0.131 -0.097 0.613 4.398 -19.703 -10.993 9 A_DA10:DT19_B A 10 ? B 19 ? 20 1 1 A DA 11 1_555 B DT 4 1_555 0.026 -0.112 0.654 6.488 -16.947 -10.922 10 A_DA11:DT18_B A 11 ? B 18 ? 20 1 1 A DA 12 1_555 B DT 3 1_555 0.131 -0.120 0.931 12.386 -11.884 -9.765 11 A_DA12:DT17_B A 12 ? B 17 ? 20 1 1 A DC 13 1_555 B DG 2 1_555 -0.209 -0.095 0.646 3.501 -9.281 -5.012 12 A_DC13:DG16_B A 13 ? B 16 ? 19 1 1 A DG 14 1_555 B DC 1 1_555 0.316 -0.087 0.961 21.833 -9.126 -6.731 13 A_DG14:DC15_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 DG 1 1_555 B DC 14 1_555 A DC 2 1_555 B DG 13 1_555 0.220 -0.376 3.542 1.010 -6.083 38.537 0.239 -0.196 3.562 -9.145 -1.519 39.009 1 AA_DG1DC2:DG27DC28_BB A 1 ? B 28 ? A 2 ? B 27 ? 1 A DC 2 1_555 B DG 13 1_555 A DA 3 1_555 B DT 12 1_555 -0.168 -0.351 2.674 3.580 -4.233 37.184 -0.092 0.644 2.669 -6.593 -5.577 37.581 2 AA_DC2DA3:DT26DG27_BB A 2 ? B 27 ? A 3 ? B 26 ? 1 A DA 3 1_555 B DT 12 1_555 A DA 4 1_555 B DT 11 1_555 -0.286 -0.781 3.062 -1.214 -3.486 35.653 -0.794 0.299 3.129 -5.674 1.976 35.837 3 AA_DA3DA4:DT25DT26_BB A 3 ? B 26 ? A 4 ? B 25 ? 1 A DA 4 1_555 B DT 11 1_555 A DG 5 1_555 B DC 10 1_555 0.277 -0.917 3.135 -0.893 -3.663 33.823 -0.999 -0.611 3.206 -6.272 1.529 34.027 4 AA_DA4DG5:DC24DT25_BB A 4 ? B 25 ? A 5 ? B 24 ? 1 A DG 5 1_555 B DC 10 1_555 A DT 6 1_555 B DA 9 1_555 -0.119 -0.717 3.444 2.233 -5.443 37.446 -0.359 0.489 3.498 -8.414 -3.452 37.889 5 AA_DG5DT6:DA23DC24_BB A 5 ? B 24 ? A 6 ? B 23 ? 1 A DT 6 1_555 B DA 9 1_555 A DC 7 1_555 B DG 8 1_555 0.218 -0.243 3.027 0.587 -3.957 39.350 0.072 -0.259 3.039 -5.858 -0.869 39.545 6 AA_DT6DC7:DG22DA23_BB A 6 ? B 23 ? A 7 ? B 22 ? 1 A DC 7 1_555 B DG 8 1_555 A DA 9 1_555 B DT 6 1_555 -0.163 -0.583 7.359 0.573 -13.000 70.630 0.500 0.183 7.358 -11.150 -0.492 71.665 7 AA_DC7DA9:DT20DG22_BB A 7 ? B 22 ? A 9 ? B 20 ? 1 A DA 9 1_555 B DT 6 1_555 A DA 10 1_555 B DT 5 1_555 0.051 -0.795 3.178 1.905 -0.746 34.723 -1.219 0.198 3.192 -1.248 -3.188 34.781 8 AA_DA9DA10:DT19DT20_BB A 9 ? B 20 ? A 10 ? B 19 ? 1 A DA 10 1_555 B DT 5 1_555 A DA 11 1_555 B DT 4 1_555 0.061 -0.729 3.068 -0.394 -3.458 35.799 -0.713 -0.152 3.121 -5.610 0.640 35.962 9 AA_DA10DA11:DT18DT19_BB A 10 ? B 19 ? A 11 ? B 18 ? 1 A DA 11 1_555 B DT 4 1_555 A DA 12 1_555 B DT 3 1_555 -0.015 -0.729 2.976 -2.650 -4.991 37.261 -0.531 -0.294 3.039 -7.757 4.118 37.672 10 AA_DA11DA12:DT17DT18_BB A 11 ? B 18 ? A 12 ? B 17 ? 1 A DA 12 1_555 B DT 3 1_555 A DC 13 1_555 B DG 2 1_555 0.026 -0.971 3.449 0.589 -3.076 35.029 -1.118 0.051 3.519 -5.098 -0.977 35.164 11 AA_DA12DC13:DG16DT17_BB A 12 ? B 17 ? A 13 ? B 16 ? 1 A DC 13 1_555 B DG 2 1_555 A DG 14 1_555 B DC 1 1_555 -0.095 -0.382 2.702 -3.060 -3.975 37.642 -0.164 -0.179 2.726 -6.127 4.717 37.963 12 AA_DC13DG14:DC15DG16_BB A 13 ? B 16 ? A 14 ? B 15 ? #