data_1K8N # _entry.id 1K8N # _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 1K8N pdb_00001k8n 10.2210/pdb1k8n/pdb RCSB RCSB014697 ? ? WWPDB D_1000014697 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1K8J 'NMR Structure of CK14, the non-thioated analog of XBY6' unspecified PDB 1K8L 'NMR Structure of CK14, an analog with 6 phosphorodithioates' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1K8N _pdbx_database_status.recvd_initial_deposition_date 2001-10-24 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Volk, D.E.' 1 'Yang, X.' 2 'Fennewald, S.M.' 3 'King, D.J.' 4 'Bassett, S.E.' 5 'Venkitachalam, S.' 6 'Herzog, N.' 7 'Luxon, B.A.' 8 'Gorenstein, D.G.' 9 # _citation.id primary _citation.title 'Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB' _citation.journal_abbrev Bioorg.Chem. _citation.journal_volume 30 _citation.page_first 396 _citation.page_last 419 _citation.year 2002 _citation.journal_id_ASTM BOCMBM _citation.country US _citation.journal_id_ISSN 0045-2068 _citation.journal_id_CSD 0368 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12642125 _citation.pdbx_database_id_DOI '10.1016/S0045-2068(02)00510-2' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Volk, D.E.' 1 ? primary 'Yang, X.' 2 ? primary 'Fennewald, S.M.' 3 ? primary 'King, D.J.' 4 ? primary 'Bassett, S.E.' 5 ? primary 'Venkitachalam, S.' 6 ? primary 'Herzog, N.' 7 ? primary 'Luxon, B.A.' 8 ? primary 'Gorenstein, D.G.' 9 ? # 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 'FIRST STRAND OF CK14 DNA DUPLEX' 4249.781 1 ? ? ? 'CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1' 2 polymer syn 'SECOND STRAND OF CK14 DNA DUPLEX' 4376.063 1 ? 'DITHIOATED AT C22 and C24' 'DITHIOATED AT C22 and C24' 'CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1' # 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 no '(DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DT)(DT)(DC)(DC)(DA)(DC)' CCAGGAGATTCCAC A ? 2 polydeoxyribonucleotide no yes '(DG)(DT)(DG)(DG)(DA)(DA)(DT)(C2S)(DT)(C2S)(DC)(DT)(DG)(DG)' GTGGAATCTCCTGG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DA n 1 4 DG n 1 5 DG n 1 6 DA n 1 7 DG n 1 8 DA n 1 9 DT n 1 10 DT n 1 11 DC n 1 12 DC n 1 13 DA n 1 14 DC n 2 1 DG n 2 2 DT n 2 3 DG n 2 4 DG n 2 5 DA n 2 6 DA n 2 7 DT n 2 8 C2S n 2 9 DT n 2 10 C2S n 2 11 DC n 2 12 DT n 2 13 DG n 2 14 DG n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'SYNTHESIZED WITH NORMAL PHOSPHOROAMIDITE CHEMISTRY' 2 1 sample ? ? ? ? ? 'SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY' # 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 1K8N 1K8N ? ? ? 2 2 PDB 1K8N 1K8N ? ? ? # 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 1K8N A 1 ? 14 ? 1K8N 1 ? 14 ? 1 14 2 2 1K8N B 1 ? 14 ? 1K8N 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 C2S 'DNA linking' n "CYTIDINE-5'-DITHIOPHOSPHORATE" ? 'C9 H14 N3 O5 P S2' 339.328 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 # 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' 2 2 2 '2D NOESY' 3 2 1 DQF-COSY # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 278 ambient 6.7 '100 mM' ? K 2 288 ambient 6.7 '100 mM' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1 mM duplex, 12 mM Na2HPO4, 8 mM NaH2PO4, 56 mM NaCl, 50 uM NaN3' '90% H2O/10% D2O' 2 '1 mM duplex, 12 mM Na2HPO4,8 mM NaH2PO4, 56 mM NaCl, 50 uM NaN3' '99.96% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Varian UNITYPLUS 750 2 ? Varian UNITYPLUS 600 # _pdbx_nmr_refine.entry_id 1K8N _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ;Distance restraints were derived by MORASS 2.5 using a total relaxation matrix method. The deposited structure represents the average of 10 final structures ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1K8N _pdbx_nmr_details.text 'Standard 2D homonuclear methods were used' # _pdbx_nmr_ensemble.entry_id 1K8N _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest 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 ? # _pdbx_nmr_representative.entry_id 1K8N _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal MORASS 2.5 'iterative matrix relaxation' Gorenstein 1 Amber 5 'structure solution' 'Case and Kollman' 2 Amber 5 refinement 'Case and Kollman' 3 # _exptl.entry_id 1K8N _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1K8N _struct.title 'NMR structure of the XBY2 DNA duplex, an analog of CK14 containing phosphorodithioate groups at C22 and C24' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1K8N _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'phosphorodithioate, CK14, CK1, NF-kB, XBY6, XBY2, thiophosphate, 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.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 ? B DT 7 "O3'" ? ? ? 1_555 B C2S 8 P ? ? B DT 21 B C2S 22 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale2 covale both ? B C2S 8 "O3'" ? ? ? 1_555 B DT 9 P ? ? B C2S 22 B DT 23 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale3 covale both ? B DT 9 "O3'" ? ? ? 1_555 B C2S 10 P ? ? B DT 23 B C2S 24 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale4 covale both ? B C2S 10 "O3'" ? ? ? 1_555 B DC 11 P ? ? B C2S 24 B DC 25 1_555 ? ? ? ? ? ? ? 1.619 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 14 N1 ? ? A DC 1 B DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 14 O6 ? ? A DC 1 B DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 14 N2 ? ? A DC 1 B DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 13 N1 ? ? A DC 2 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 13 O6 ? ? A DC 2 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 13 N2 ? ? A DC 2 B DG 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 12 N3 ? ? A DA 3 B DT 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 12 O4 ? ? A DA 3 B DT 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 4 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 4 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 4 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B C2S 10 N3 ? ? A DG 5 B C2S 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B C2S 10 O2 ? ? A DG 5 B C2S 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B C2S 10 N4 ? ? A DG 5 B C2S 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 6 B DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 6 B DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B C2S 8 N3 ? ? A DG 7 B C2S 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B C2S 8 O2 ? ? A DG 7 B C2S 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B C2S 8 N4 ? ? A DG 7 B C2S 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 8 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 8 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 9 B DA 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 9 B DA 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 10 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 10 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 12 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 12 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 12 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DA 13 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 13 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DA 13 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 13 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DC 14 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 14 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DC 14 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 14 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DC 14 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 14 B DG 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 1K8N _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 1K8N _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 S # 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 DC 1 1 1 DC C 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 DG 4 4 4 DG G A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DT 10 10 10 DT T A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DC 12 12 12 DC C A . n A 1 13 DA 13 13 13 DA A A . n A 1 14 DC 14 14 14 DC C A . n B 2 1 DG 1 15 15 DG G B . n B 2 2 DT 2 16 16 DT T B . n B 2 3 DG 3 17 17 DG G B . n B 2 4 DG 4 18 18 DG G B . n B 2 5 DA 5 19 19 DA A B . n B 2 6 DA 6 20 20 DA A B . n B 2 7 DT 7 21 21 DT T B . n B 2 8 C2S 8 22 22 C2S C2S B . n B 2 9 DT 9 23 23 DT T B . n B 2 10 C2S 10 24 24 C2S C2S B . n B 2 11 DC 11 25 25 DC C 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 DG 14 28 28 DG G B . n # 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 B C2S 8 B C2S 22 ? DC "CYTIDINE-5'-DITHIOPHOSPHORATE" 2 B C2S 10 B C2S 24 ? DC "CYTIDINE-5'-DITHIOPHOSPHORATE" # _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 2003-04-15 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_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 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' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "HO5'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DC _pdbx_validate_close_contact.auth_seq_id_1 1 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OP2 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 DC _pdbx_validate_close_contact.auth_seq_id_2 2 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.33 # 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 DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 113.80 108.30 5.50 0.30 N 2 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 112.46 108.30 4.16 0.30 N 3 1 C5 A DA 3 ? ? C6 A DA 3 ? ? N1 A DA 3 ? ? 121.05 117.70 3.35 0.50 N 4 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 113.75 108.30 5.45 0.30 N 5 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 112.35 108.30 4.05 0.30 N 6 1 N1 A DA 6 ? ? C6 A DA 6 ? ? N6 A DA 6 ? ? 114.96 118.60 -3.64 0.60 N 7 1 "O4'" A DC 12 ? ? "C1'" A DC 12 ? ? N1 A DC 12 ? ? 112.29 108.30 3.99 0.30 N 8 1 "O4'" B DG 15 ? ? "C1'" B DG 15 ? ? N9 B DG 15 ? ? 111.51 108.30 3.21 0.30 N 9 1 "O4'" B DG 18 ? ? "C1'" B DG 18 ? ? N9 B DG 18 ? ? 113.22 108.30 4.92 0.30 N 10 1 "O4'" B DT 21 ? ? "C1'" B DT 21 ? ? N1 B DT 21 ? ? 112.71 108.30 4.41 0.30 N 11 1 C6 B DT 21 ? ? C5 B DT 21 ? ? C7 B DT 21 ? ? 119.14 122.90 -3.76 0.60 N 12 1 "O4'" B DT 23 ? ? "C1'" B DT 23 ? ? N1 B DT 23 ? ? 110.94 108.30 2.64 0.30 N 13 1 C6 B DT 23 ? ? C5 B DT 23 ? ? C7 B DT 23 ? ? 119.03 122.90 -3.87 0.60 N 14 1 "O4'" B DC 25 ? ? "C1'" B DC 25 ? ? N1 B DC 25 ? ? 112.13 108.30 3.83 0.30 N 15 1 "O4'" B DT 26 ? ? "C1'" B DT 26 ? ? N1 B DT 26 ? ? 110.20 108.30 1.90 0.30 N 16 1 "O4'" B DG 27 ? ? "C1'" B DG 27 ? ? N9 B DG 27 ? ? 114.47 108.30 6.17 0.30 N 17 1 "O4'" B DG 28 ? ? "C1'" B DG 28 ? ? N9 B DG 28 ? ? 110.82 108.30 2.52 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 DC A 1 ? ? 0.063 'SIDE CHAIN' 2 1 DC A 2 ? ? 0.067 'SIDE CHAIN' 3 1 DG A 4 ? ? 0.059 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1K8N 'double helix' 1K8N '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 DC 1 1_555 B DG 14 1_555 0.650 -0.140 -0.607 33.540 -17.943 1.266 1 A_DC1:DG28_B A 1 ? B 28 ? 19 1 1 A DC 2 1_555 B DG 13 1_555 0.386 -0.226 -0.315 3.532 8.410 -1.320 2 A_DC2:DG27_B A 2 ? B 27 ? 19 1 1 A DA 3 1_555 B DT 12 1_555 0.412 -0.015 -0.282 -2.377 -1.949 -5.926 3 A_DA3:DT26_B A 3 ? B 26 ? 20 1 1 A DG 4 1_555 B DC 11 1_555 -0.447 -0.211 -0.063 11.403 0.047 0.826 4 A_DG4:DC25_B A 4 ? B 25 ? 19 1 1 A DG 5 1_555 B C2S 10 1_555 -0.302 -0.145 0.291 17.891 4.489 -0.719 5 A_DG5:C2S24_B A 5 ? B 24 ? 19 1 1 A DA 6 1_555 B DT 9 1_555 0.043 -0.143 -0.219 17.601 -13.297 1.959 6 A_DA6:DT23_B A 6 ? B 23 ? 20 1 1 A DG 7 1_555 B C2S 8 1_555 -0.294 -0.197 -0.138 2.674 -4.831 -0.823 7 A_DG7:C2S22_B A 7 ? B 22 ? 19 1 1 A DA 8 1_555 B DT 7 1_555 0.073 -0.109 0.083 4.209 -11.873 -2.042 8 A_DA8:DT21_B A 8 ? B 21 ? 20 1 1 A DT 9 1_555 B DA 6 1_555 -0.166 -0.094 0.039 -1.331 -12.268 -4.791 9 A_DT9:DA20_B A 9 ? B 20 ? 20 1 1 A DT 10 1_555 B DA 5 1_555 -0.183 -0.099 -0.198 -0.607 -12.855 -2.865 10 A_DT10:DA19_B A 10 ? B 19 ? 20 1 1 A DC 11 1_555 B DG 4 1_555 0.338 -0.211 -0.055 -8.160 -3.718 -0.723 11 A_DC11:DG18_B A 11 ? B 18 ? 19 1 1 A DC 12 1_555 B DG 3 1_555 0.384 -0.206 0.175 -6.008 -1.402 -0.014 12 A_DC12:DG17_B A 12 ? B 17 ? 19 1 1 A DA 13 1_555 B DT 2 1_555 0.108 -0.115 0.058 4.726 -6.327 -1.609 13 A_DA13:DT16_B A 13 ? B 16 ? 20 1 1 A DC 14 1_555 B DG 1 1_555 0.507 -0.240 0.207 0.610 -4.148 -0.040 14 A_DC14:DG15_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 DC 1 1_555 B DG 14 1_555 A DC 2 1_555 B DG 13 1_555 0.473 -1.336 6.281 -7.874 -2.156 37.194 -1.523 -2.645 6.124 -3.331 12.165 38.049 1 AA_DC1DC2:DG27DG28_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 -1.595 -0.560 3.597 -1.511 -3.284 33.594 -0.369 2.472 3.700 -5.661 2.604 33.783 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 DG 4 1_555 B DC 11 1_555 1.125 -1.021 3.144 -3.947 -3.753 23.119 -1.296 -3.981 3.037 -9.200 9.678 23.744 3 AA_DA3DG4:DC25DT26_BB A 3 ? B 26 ? A 4 ? B 25 ? 1 A DG 4 1_555 B DC 11 1_555 A DG 5 1_555 B C2S 10 1_555 -1.076 -0.684 3.252 -6.157 -5.857 38.174 -0.293 0.841 3.442 -8.822 9.274 39.073 4 AA_DG4DG5:C2S24DC25_BB A 4 ? B 25 ? A 5 ? B 24 ? 1 A DG 5 1_555 B C2S 10 1_555 A DA 6 1_555 B DT 9 1_555 -0.025 -1.246 3.356 1.298 8.565 27.023 -4.460 0.342 2.832 17.758 -2.692 28.352 5 AA_DG5DA6:DT23C2S24_BB A 5 ? B 24 ? A 6 ? B 23 ? 1 A DA 6 1_555 B DT 9 1_555 A DG 7 1_555 B C2S 8 1_555 -1.883 -0.182 3.398 -8.820 13.604 37.351 -1.926 1.636 3.472 20.122 13.045 40.603 6 AA_DA6DG7:C2S22DT23_BB A 6 ? B 23 ? A 7 ? B 22 ? 1 A DG 7 1_555 B C2S 8 1_555 A DA 8 1_555 B DT 7 1_555 0.099 -0.284 3.265 -3.151 6.870 34.520 -1.474 -0.625 3.132 11.408 5.232 35.313 7 AA_DG7DA8:DT21C2S22_BB A 7 ? B 22 ? A 8 ? B 21 ? 1 A DA 8 1_555 B DT 7 1_555 A DT 9 1_555 B DA 6 1_555 -0.750 -1.136 3.384 -0.880 2.522 29.680 -2.747 1.270 3.298 4.912 1.714 29.797 8 AA_DA8DT9:DA20DT21_BB A 8 ? B 21 ? A 9 ? B 20 ? 1 A DT 9 1_555 B DA 6 1_555 A DT 10 1_555 B DA 5 1_555 0.018 -0.373 3.154 2.734 1.108 37.563 -0.715 0.313 3.136 1.717 -4.238 37.675 9 AA_DT9DT10:DA19DA20_BB A 9 ? B 20 ? A 10 ? B 19 ? 1 A DT 10 1_555 B DA 5 1_555 A DC 11 1_555 B DG 4 1_555 0.611 0.257 3.410 0.596 2.338 46.561 0.120 -0.720 3.426 2.956 -0.753 46.620 10 AA_DT10DC11:DG18DA19_BB A 10 ? B 19 ? A 11 ? B 18 ? 1 A DC 11 1_555 B DG 4 1_555 A DC 12 1_555 B DG 3 1_555 -0.118 -1.014 3.256 -1.519 0.742 25.386 -2.515 -0.166 3.227 1.687 3.451 25.442 11 AA_DC11DC12:DG17DG18_BB A 11 ? B 18 ? A 12 ? B 17 ? 1 A DC 12 1_555 B DG 3 1_555 A DA 13 1_555 B DT 2 1_555 0.444 0.294 2.993 5.649 1.565 38.721 0.264 -0.036 3.035 2.344 -8.461 39.145 12 AA_DC12DA13:DT16DG17_BB A 12 ? B 17 ? A 13 ? B 16 ? 1 A DA 13 1_555 B DT 2 1_555 A DC 14 1_555 B DG 1 1_555 0.214 -0.949 3.482 -3.851 -5.175 42.001 -0.744 -0.717 3.537 -7.170 5.335 42.471 13 AA_DA13DC14:DG15DT16_BB A 13 ? B 16 ? A 14 ? B 15 ? #