data_1K8L # _entry.id 1K8L # _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 1K8L pdb_00001k8l 10.2210/pdb1k8l/pdb RCSB RCSB014695 ? ? WWPDB D_1000014695 ? ? # 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 5 'Structure model' 1 4 2022-06-22 6 'Structure model' 1 5 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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Derived calculations' 7 6 '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' chem_comp 2 4 'Structure model' database_2 3 4 'Structure model' pdbx_nmr_software 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' struct_conn 7 5 'Structure model' pdbx_struct_mod_residue 8 6 'Structure model' chem_comp_atom 9 6 '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' '_chem_comp.type' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_pdbx_nmr_software.name' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 5 'Structure model' '_pdbx_struct_mod_residue.parent_comp_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1K8L _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.status_code_sf ? _pdbx_database_status.SG_entry ? _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_ _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 1K8N 'NMR Structure of CK14, an analog with 2 phosphorodithioates' unspecified # 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' 4314.044 1 ? 'DITHIOATED AT T10, C11' 'DITHIOATED AT T10, C11' 'CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1' 2 polymer syn 'SECOND STRAND OF CK14 DNA DUPLEX' 4440.326 1 ? 'DITHIOATED AT G17, C22, C24, G27' 'DITHIOATED AT G17, C22, C24, G27' '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 yes '(DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DT)(T2S)(C2S)(DC)(DA)(DC)' CCAGGAGATTCCAC A ? 2 polydeoxyribonucleotide no yes '(DG)(DT)(G2S)(DG)(DA)(DA)(DT)(C2S)(DT)(C2S)(DC)(DT)(G2S)(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 T2S n 1 11 C2S n 1 12 DC n 1 13 DA n 1 14 DC n 2 1 DG n 2 2 DT n 2 3 G2S 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 G2S 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 BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY' 2 1 sample ? ? ? ? ? 'SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY' # 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 G2S 'DNA linking' n "GUANOSINE-5'-DITHIOPHOSPHORATE" ? 'C10 H14 N5 O5 P S2' 379.352 T2S 'DNA linking' n "THYMIDINE-5'-DITHIOPHOSPHORATE" ? 'C10 H15 N2 O6 P S2' 354.340 # 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 T2S 10 10 10 T2S T2S A . n A 1 11 C2S 11 11 11 C2S C2S 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 G2S 3 17 17 G2S G2S 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 G2S 13 27 27 G2S G2S B . n B 2 14 DG 14 28 28 DG G B . n # _exptl.entry_id 1K8L _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 1K8L _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 1K8L _struct.title 'XBY6: An analog of CK14 containing 6 dithiophosphate groups' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1K8L _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'XBY6, CK14, CK1, PHOSPHORODITHIOATE, NF-KB, 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 ? # 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 1K8L 1K8L ? ? ? 2 2 PDB 1K8L 1K8L ? ? ? # 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 1K8L A 1 ? 14 ? 1K8L 1 ? 14 ? 1 14 2 2 1K8L B 1 ? 14 ? 1K8L 15 ? 28 ? 15 28 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 both ? A DT 9 "O3'" ? ? ? 1_555 A T2S 10 P ? ? A DT 9 A T2S 10 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale2 covale both ? A T2S 10 "O3'" ? ? ? 1_555 A C2S 11 P ? ? A T2S 10 A C2S 11 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale3 covale both ? A C2S 11 "O3'" ? ? ? 1_555 A DC 12 P ? ? A C2S 11 A DC 12 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale4 covale both ? B DT 2 "O3'" ? ? ? 1_555 B G2S 3 P ? ? B DT 16 B G2S 17 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale5 covale both ? B G2S 3 "O3'" ? ? ? 1_555 B DG 4 P ? ? B G2S 17 B DG 18 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale6 covale both ? B DT 7 "O3'" ? ? ? 1_555 B C2S 8 P ? ? B DT 21 B C2S 22 1_555 ? ? ? ? ? ? ? 1.622 ? ? covale7 covale both ? B C2S 8 "O3'" ? ? ? 1_555 B DT 9 P ? ? B C2S 22 B DT 23 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale8 covale both ? B DT 9 "O3'" ? ? ? 1_555 B C2S 10 P ? ? B DT 23 B C2S 24 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale9 covale both ? B C2S 10 "O3'" ? ? ? 1_555 B DC 11 P ? ? B C2S 24 B DC 25 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale10 covale both ? B DT 12 "O3'" ? ? ? 1_555 B G2S 13 P ? ? B DT 26 B G2S 27 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale11 covale both ? B G2S 13 "O3'" ? ? ? 1_555 B DG 14 P ? ? B G2S 27 B DG 28 1_555 ? ? ? ? ? ? ? 1.611 ? ? 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 G2S 13 N1 ? ? A DC 2 B G2S 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B G2S 13 O6 ? ? A DC 2 B G2S 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B G2S 13 N2 ? ? A DC 2 B G2S 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 T2S 10 N3 ? ? ? 1_555 B DA 5 N1 ? ? A T2S 10 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A T2S 10 O4 ? ? ? 1_555 B DA 5 N6 ? ? A T2S 10 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C2S 11 N3 ? ? ? 1_555 B DG 4 N1 ? ? A C2S 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C2S 11 N4 ? ? ? 1_555 B DG 4 O6 ? ? A C2S 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C2S 11 O2 ? ? ? 1_555 B DG 4 N2 ? ? A C2S 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B G2S 3 N1 ? ? A DC 12 B G2S 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B G2S 3 O6 ? ? A DC 12 B G2S 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B G2S 3 N2 ? ? A DC 12 B G2S 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 ? ? # _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 1.40 # 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 "C1'" A DC 1 ? ? "O4'" A DC 1 ? ? "C4'" A DC 1 ? ? 103.59 110.10 -6.51 1.00 N 2 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? "C1'" A DC 1 ? ? 97.19 102.40 -5.21 0.80 N 3 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.44 105.90 -5.46 0.80 N 4 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 115.13 108.30 6.83 0.30 N 5 1 N3 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 117.65 121.90 -4.25 0.70 N 6 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 112.27 108.30 3.97 0.30 N 7 1 C5 A DA 3 ? ? C6 A DA 3 ? ? N1 A DA 3 ? ? 120.92 117.70 3.22 0.50 N 8 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.17 108.30 2.87 0.30 N 9 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.22 108.30 1.92 0.30 N 10 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 112.14 108.30 3.84 0.30 N 11 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 112.30 108.30 4.00 0.30 N 12 1 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.16 122.90 -3.74 0.60 N 13 1 "O4'" B DG 15 ? ? "C1'" B DG 15 ? ? N9 B DG 15 ? ? 111.13 108.30 2.83 0.30 N 14 1 "O4'" B DA 19 ? ? "C1'" B DA 19 ? ? N9 B DA 19 ? ? 110.62 108.30 2.32 0.30 N 15 1 "O4'" B DT 21 ? ? "C1'" B DT 21 ? ? N1 B DT 21 ? ? 113.10 108.30 4.80 0.30 N 16 1 C6 B DT 21 ? ? C5 B DT 21 ? ? C7 B DT 21 ? ? 119.09 122.90 -3.81 0.60 N 17 1 "O4'" B DT 23 ? ? "C1'" B DT 23 ? ? N1 B DT 23 ? ? 110.16 108.30 1.86 0.30 N 18 1 C6 B DT 23 ? ? C5 B DT 23 ? ? C7 B DT 23 ? ? 118.90 122.90 -4.00 0.60 N 19 1 "O4'" B DG 28 ? ? "C1'" B DG 28 ? ? N9 B DG 28 ? ? 110.36 108.30 2.06 0.30 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 A T2S 10 A T2S 10 ? DT "THYMIDINE-5'-DITHIOPHOSPHORATE" 2 A C2S 11 A C2S 11 ? DC "CYTIDINE-5'-DITHIOPHOSPHORATE" 3 B G2S 3 B G2S 17 ? DG "GUANOSINE-5'-DITHIOPHOSPHORATE" 4 B C2S 8 B C2S 22 ? DC "CYTIDINE-5'-DITHIOPHOSPHORATE" 5 B C2S 10 B C2S 24 ? DC "CYTIDINE-5'-DITHIOPHOSPHORATE" 6 B G2S 13 B G2S 27 ? DG "GUANOSINE-5'-DITHIOPHOSPHORATE" # _pdbx_nmr_ensemble.entry_id 1K8L _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 1K8L _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # 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, 56mM NaCl, 50 uM NaN3' '99.96% D2O' # 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_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 2 1 '2D NOESY' 3 2 2 DQF-COSY # _pdbx_nmr_details.entry_id 1K8L _pdbx_nmr_details.text ;This structure was determined using standard 2D homonuclear techniques. Proton resonances were assigned using COSY, TOCSY, and NOESY data ; # _pdbx_nmr_refine.entry_id 1K8L _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ;Distance restraints were derived by MORASS 2.5 using a total relaxation matrix approach. AMBER 5 was used for MD and minimization. The deposited structure represents the average of ten final structures ; _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 MORASS 2.5 'iterative matrix relaxation' Gorenstein 1 Amber 5 'structure solution' 'Case,Kollman, et al' 2 Amber 5 refinement 'Case,Kollman, et al' 3 # 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 C2S OP3 O N N 1 C2S P P N S 2 C2S S1P S N N 3 C2S S2P S N N 4 C2S "O5'" O N N 5 C2S "C5'" C N N 6 C2S "C4'" C N R 7 C2S "O4'" O N N 8 C2S "C3'" C N S 9 C2S "O3'" O N N 10 C2S "C2'" C N N 11 C2S "C1'" C N R 12 C2S N1 N N N 13 C2S C2 C N N 14 C2S O2 O N N 15 C2S N3 N N N 16 C2S C4 C N N 17 C2S N4 N N N 18 C2S C5 C N N 19 C2S C6 C N N 20 C2S HOP3 H N N 21 C2S HOP2 H N N 22 C2S "H5'" H N N 23 C2S "H5''" H N N 24 C2S "H4'" H N N 25 C2S "H3'" H N N 26 C2S "HO3'" H N N 27 C2S "H2'1" H N N 28 C2S "H1'" H N N 29 C2S H41 H N N 30 C2S H42 H N N 31 C2S H5 H N N 32 C2S H6 H N N 33 C2S "H2'2" H N N 34 DA OP3 O N N 35 DA P P N N 36 DA OP1 O N N 37 DA OP2 O N N 38 DA "O5'" O N N 39 DA "C5'" C N N 40 DA "C4'" C N R 41 DA "O4'" O N N 42 DA "C3'" C N S 43 DA "O3'" O N N 44 DA "C2'" C N N 45 DA "C1'" C N R 46 DA N9 N Y N 47 DA C8 C Y N 48 DA N7 N Y N 49 DA C5 C Y N 50 DA C6 C Y N 51 DA N6 N N N 52 DA N1 N Y N 53 DA C2 C Y N 54 DA N3 N Y N 55 DA C4 C Y N 56 DA HOP3 H N N 57 DA HOP2 H N N 58 DA "H5'" H N N 59 DA "H5''" H N N 60 DA "H4'" H N N 61 DA "H3'" H N N 62 DA "HO3'" H N N 63 DA "H2'" H N N 64 DA "H2''" H N N 65 DA "H1'" H N N 66 DA H8 H N N 67 DA H61 H N N 68 DA H62 H N N 69 DA H2 H N N 70 DC OP3 O N N 71 DC P P N N 72 DC OP1 O N N 73 DC OP2 O N N 74 DC "O5'" O N N 75 DC "C5'" C N N 76 DC "C4'" C N R 77 DC "O4'" O N N 78 DC "C3'" C N S 79 DC "O3'" O N N 80 DC "C2'" C N N 81 DC "C1'" C N R 82 DC N1 N N N 83 DC C2 C N N 84 DC O2 O N N 85 DC N3 N N N 86 DC C4 C N N 87 DC N4 N N N 88 DC C5 C N N 89 DC C6 C N N 90 DC HOP3 H N N 91 DC HOP2 H N N 92 DC "H5'" H N N 93 DC "H5''" H N N 94 DC "H4'" H N N 95 DC "H3'" H N N 96 DC "HO3'" H N N 97 DC "H2'" H N N 98 DC "H2''" H N N 99 DC "H1'" H N N 100 DC H41 H N N 101 DC H42 H N N 102 DC H5 H N N 103 DC H6 H N N 104 DG OP3 O N N 105 DG P P N N 106 DG OP1 O N N 107 DG OP2 O N N 108 DG "O5'" O N N 109 DG "C5'" C N N 110 DG "C4'" C N R 111 DG "O4'" O N N 112 DG "C3'" C N S 113 DG "O3'" O N N 114 DG "C2'" C N N 115 DG "C1'" C N R 116 DG N9 N Y N 117 DG C8 C Y N 118 DG N7 N Y N 119 DG C5 C Y N 120 DG C6 C N N 121 DG O6 O N N 122 DG N1 N N N 123 DG C2 C N N 124 DG N2 N N N 125 DG N3 N N N 126 DG C4 C Y N 127 DG HOP3 H N N 128 DG HOP2 H N N 129 DG "H5'" H N N 130 DG "H5''" H N N 131 DG "H4'" H N N 132 DG "H3'" H N N 133 DG "HO3'" H N N 134 DG "H2'" H N N 135 DG "H2''" H N N 136 DG "H1'" H N N 137 DG H8 H N N 138 DG H1 H N N 139 DG H21 H N N 140 DG H22 H N N 141 DT OP3 O N N 142 DT P P N N 143 DT OP1 O N N 144 DT OP2 O N N 145 DT "O5'" O N N 146 DT "C5'" C N N 147 DT "C4'" C N R 148 DT "O4'" O N N 149 DT "C3'" C N S 150 DT "O3'" O N N 151 DT "C2'" C N N 152 DT "C1'" C N R 153 DT N1 N N N 154 DT C2 C N N 155 DT O2 O N N 156 DT N3 N N N 157 DT C4 C N N 158 DT O4 O N N 159 DT C5 C N N 160 DT C7 C N N 161 DT C6 C N N 162 DT HOP3 H N N 163 DT HOP2 H N N 164 DT "H5'" H N N 165 DT "H5''" H N N 166 DT "H4'" H N N 167 DT "H3'" H N N 168 DT "HO3'" H N N 169 DT "H2'" H N N 170 DT "H2''" H N N 171 DT "H1'" H N N 172 DT H3 H N N 173 DT H71 H N N 174 DT H72 H N N 175 DT H73 H N N 176 DT H6 H N N 177 G2S OP3 O N N 178 G2S P P N R 179 G2S S1P S N N 180 G2S S2P S N N 181 G2S "O5'" O N N 182 G2S "C5'" C N N 183 G2S "C4'" C N R 184 G2S "O4'" O N N 185 G2S "C3'" C N S 186 G2S "O3'" O N N 187 G2S "C2'" C N N 188 G2S "C1'" C N R 189 G2S N9 N Y N 190 G2S C8 C Y N 191 G2S N7 N Y N 192 G2S C5 C Y N 193 G2S C6 C N N 194 G2S O6 O N N 195 G2S N1 N N N 196 G2S C2 C N N 197 G2S N2 N N N 198 G2S N3 N N N 199 G2S C4 C Y N 200 G2S HOP3 H N N 201 G2S HOP2 H N N 202 G2S "H5'" H N N 203 G2S "H5''" H N N 204 G2S "H4'" H N N 205 G2S "H3'" H N N 206 G2S "HO3'" H N N 207 G2S "H2'1" H N N 208 G2S "H1'" H N N 209 G2S H8 H N N 210 G2S H1 H N N 211 G2S H21 H N N 212 G2S H22 H N N 213 G2S "H2'2" H N N 214 T2S OP3 O N N 215 T2S P P N S 216 T2S S1P S N N 217 T2S S2P S N N 218 T2S "O5'" O N N 219 T2S "C5'" C N N 220 T2S "C4'" C N R 221 T2S "O4'" O N N 222 T2S "C3'" C N S 223 T2S "O3'" O N N 224 T2S "C2'" C N N 225 T2S "C1'" C N R 226 T2S N1 N N N 227 T2S C2 C N N 228 T2S O2 O N N 229 T2S N3 N N N 230 T2S C4 C N N 231 T2S O4 O N N 232 T2S C5 C N N 233 T2S C5M C N N 234 T2S C6 C N N 235 T2S HOP3 H N N 236 T2S HOP2 H N N 237 T2S "H5'" H N N 238 T2S "H5''" H N N 239 T2S "H4'" H N N 240 T2S "H3'" H N N 241 T2S "HO3'" H N N 242 T2S "H2'" H N N 243 T2S "H2''" H N N 244 T2S "H1'" H N N 245 T2S H3 H N N 246 T2S H71 H N N 247 T2S H72 H N N 248 T2S H73 H N N 249 T2S H6 H N N 250 # 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 C2S OP3 P sing N N 1 C2S OP3 HOP3 sing N N 2 C2S P S1P doub N N 3 C2S P S2P sing N N 4 C2S P "O5'" sing N N 5 C2S S2P HOP2 sing N N 6 C2S "O5'" "C5'" sing N N 7 C2S "C5'" "C4'" sing N N 8 C2S "C5'" "H5'" sing N N 9 C2S "C5'" "H5''" sing N N 10 C2S "C4'" "O4'" sing N N 11 C2S "C4'" "C3'" sing N N 12 C2S "C4'" "H4'" sing N N 13 C2S "O4'" "C1'" sing N N 14 C2S "C3'" "O3'" sing N N 15 C2S "C3'" "C2'" sing N N 16 C2S "C3'" "H3'" sing N N 17 C2S "O3'" "HO3'" sing N N 18 C2S "C2'" "C1'" sing N N 19 C2S "C2'" "H2'1" sing N N 20 C2S "C1'" N1 sing N N 21 C2S "C1'" "H1'" sing N N 22 C2S N1 C2 sing N N 23 C2S N1 C6 sing N N 24 C2S C2 O2 doub N N 25 C2S C2 N3 sing N N 26 C2S N3 C4 doub N N 27 C2S C4 N4 sing N N 28 C2S C4 C5 sing N N 29 C2S N4 H41 sing N N 30 C2S N4 H42 sing N N 31 C2S C5 C6 doub N N 32 C2S C5 H5 sing N N 33 C2S C6 H6 sing N N 34 C2S "C2'" "H2'2" sing N N 35 DA OP3 P sing N N 36 DA OP3 HOP3 sing N N 37 DA P OP1 doub N N 38 DA P OP2 sing N N 39 DA P "O5'" sing N N 40 DA OP2 HOP2 sing N N 41 DA "O5'" "C5'" sing N N 42 DA "C5'" "C4'" sing N N 43 DA "C5'" "H5'" sing N N 44 DA "C5'" "H5''" sing N N 45 DA "C4'" "O4'" sing N N 46 DA "C4'" "C3'" sing N N 47 DA "C4'" "H4'" sing N N 48 DA "O4'" "C1'" sing N N 49 DA "C3'" "O3'" sing N N 50 DA "C3'" "C2'" sing N N 51 DA "C3'" "H3'" sing N N 52 DA "O3'" "HO3'" sing N N 53 DA "C2'" "C1'" sing N N 54 DA "C2'" "H2'" sing N N 55 DA "C2'" "H2''" sing N N 56 DA "C1'" N9 sing N N 57 DA "C1'" "H1'" sing N N 58 DA N9 C8 sing Y N 59 DA N9 C4 sing Y N 60 DA C8 N7 doub Y N 61 DA C8 H8 sing N N 62 DA N7 C5 sing Y N 63 DA C5 C6 sing Y N 64 DA C5 C4 doub Y N 65 DA C6 N6 sing N N 66 DA C6 N1 doub Y N 67 DA N6 H61 sing N N 68 DA N6 H62 sing N N 69 DA N1 C2 sing Y N 70 DA C2 N3 doub Y N 71 DA C2 H2 sing N N 72 DA N3 C4 sing Y N 73 DC OP3 P sing N N 74 DC OP3 HOP3 sing N N 75 DC P OP1 doub N N 76 DC P OP2 sing N N 77 DC P "O5'" sing N N 78 DC OP2 HOP2 sing N N 79 DC "O5'" "C5'" sing N N 80 DC "C5'" "C4'" sing N N 81 DC "C5'" "H5'" sing N N 82 DC "C5'" "H5''" sing N N 83 DC "C4'" "O4'" sing N N 84 DC "C4'" "C3'" sing N N 85 DC "C4'" "H4'" sing N N 86 DC "O4'" "C1'" sing N N 87 DC "C3'" "O3'" sing N N 88 DC "C3'" "C2'" sing N N 89 DC "C3'" "H3'" sing N N 90 DC "O3'" "HO3'" sing N N 91 DC "C2'" "C1'" sing N N 92 DC "C2'" "H2'" sing N N 93 DC "C2'" "H2''" sing N N 94 DC "C1'" N1 sing N N 95 DC "C1'" "H1'" sing N N 96 DC N1 C2 sing N N 97 DC N1 C6 sing N N 98 DC C2 O2 doub N N 99 DC C2 N3 sing N N 100 DC N3 C4 doub N N 101 DC C4 N4 sing N N 102 DC C4 C5 sing N N 103 DC N4 H41 sing N N 104 DC N4 H42 sing N N 105 DC C5 C6 doub N N 106 DC C5 H5 sing N N 107 DC C6 H6 sing N N 108 DG OP3 P sing N N 109 DG OP3 HOP3 sing N N 110 DG P OP1 doub N N 111 DG P OP2 sing N N 112 DG P "O5'" sing N N 113 DG OP2 HOP2 sing N N 114 DG "O5'" "C5'" sing N N 115 DG "C5'" "C4'" sing N N 116 DG "C5'" "H5'" sing N N 117 DG "C5'" "H5''" sing N N 118 DG "C4'" "O4'" sing N N 119 DG "C4'" "C3'" sing N N 120 DG "C4'" "H4'" sing N N 121 DG "O4'" "C1'" sing N N 122 DG "C3'" "O3'" sing N N 123 DG "C3'" "C2'" sing N N 124 DG "C3'" "H3'" sing N N 125 DG "O3'" "HO3'" sing N N 126 DG "C2'" "C1'" sing N N 127 DG "C2'" "H2'" sing N N 128 DG "C2'" "H2''" sing N N 129 DG "C1'" N9 sing N N 130 DG "C1'" "H1'" sing N N 131 DG N9 C8 sing Y N 132 DG N9 C4 sing Y N 133 DG C8 N7 doub Y N 134 DG C8 H8 sing N N 135 DG N7 C5 sing Y N 136 DG C5 C6 sing N N 137 DG C5 C4 doub Y N 138 DG C6 O6 doub N N 139 DG C6 N1 sing N N 140 DG N1 C2 sing N N 141 DG N1 H1 sing N N 142 DG C2 N2 sing N N 143 DG C2 N3 doub N N 144 DG N2 H21 sing N N 145 DG N2 H22 sing N N 146 DG N3 C4 sing N N 147 DT OP3 P sing N N 148 DT OP3 HOP3 sing N N 149 DT P OP1 doub N N 150 DT P OP2 sing N N 151 DT P "O5'" sing N N 152 DT OP2 HOP2 sing N N 153 DT "O5'" "C5'" sing N N 154 DT "C5'" "C4'" sing N N 155 DT "C5'" "H5'" sing N N 156 DT "C5'" "H5''" sing N N 157 DT "C4'" "O4'" sing N N 158 DT "C4'" "C3'" sing N N 159 DT "C4'" "H4'" sing N N 160 DT "O4'" "C1'" sing N N 161 DT "C3'" "O3'" sing N N 162 DT "C3'" "C2'" sing N N 163 DT "C3'" "H3'" sing N N 164 DT "O3'" "HO3'" sing N N 165 DT "C2'" "C1'" sing N N 166 DT "C2'" "H2'" sing N N 167 DT "C2'" "H2''" sing N N 168 DT "C1'" N1 sing N N 169 DT "C1'" "H1'" sing N N 170 DT N1 C2 sing N N 171 DT N1 C6 sing N N 172 DT C2 O2 doub N N 173 DT C2 N3 sing N N 174 DT N3 C4 sing N N 175 DT N3 H3 sing N N 176 DT C4 O4 doub N N 177 DT C4 C5 sing N N 178 DT C5 C7 sing N N 179 DT C5 C6 doub N N 180 DT C7 H71 sing N N 181 DT C7 H72 sing N N 182 DT C7 H73 sing N N 183 DT C6 H6 sing N N 184 G2S OP3 P sing N N 185 G2S OP3 HOP3 sing N N 186 G2S P S1P doub N N 187 G2S P S2P sing N N 188 G2S P "O5'" sing N N 189 G2S S2P HOP2 sing N N 190 G2S "O5'" "C5'" sing N N 191 G2S "C5'" "C4'" sing N N 192 G2S "C5'" "H5'" sing N N 193 G2S "C5'" "H5''" sing N N 194 G2S "C4'" "O4'" sing N N 195 G2S "C4'" "C3'" sing N N 196 G2S "C4'" "H4'" sing N N 197 G2S "O4'" "C1'" sing N N 198 G2S "C3'" "O3'" sing N N 199 G2S "C3'" "C2'" sing N N 200 G2S "C3'" "H3'" sing N N 201 G2S "O3'" "HO3'" sing N N 202 G2S "C2'" "C1'" sing N N 203 G2S "C2'" "H2'1" sing N N 204 G2S "C1'" N9 sing N N 205 G2S "C1'" "H1'" sing N N 206 G2S N9 C8 sing Y N 207 G2S N9 C4 sing Y N 208 G2S C8 N7 doub Y N 209 G2S C8 H8 sing N N 210 G2S N7 C5 sing Y N 211 G2S C5 C6 sing N N 212 G2S C5 C4 doub Y N 213 G2S C6 O6 doub N N 214 G2S C6 N1 sing N N 215 G2S N1 C2 sing N N 216 G2S N1 H1 sing N N 217 G2S C2 N2 sing N N 218 G2S C2 N3 doub N N 219 G2S N2 H21 sing N N 220 G2S N2 H22 sing N N 221 G2S N3 C4 sing N N 222 G2S "C2'" "H2'2" sing N N 223 T2S OP3 P sing N N 224 T2S OP3 HOP3 sing N N 225 T2S P S1P doub N N 226 T2S P S2P sing N N 227 T2S P "O5'" sing N N 228 T2S S2P HOP2 sing N N 229 T2S "O5'" "C5'" sing N N 230 T2S "C5'" "C4'" sing N N 231 T2S "C5'" "H5'" sing N N 232 T2S "C5'" "H5''" sing N N 233 T2S "C4'" "O4'" sing N N 234 T2S "C4'" "C3'" sing N N 235 T2S "C4'" "H4'" sing N N 236 T2S "O4'" "C1'" sing N N 237 T2S "C3'" "O3'" sing N N 238 T2S "C3'" "C2'" sing N N 239 T2S "C3'" "H3'" sing N N 240 T2S "O3'" "HO3'" sing N N 241 T2S "C2'" "C1'" sing N N 242 T2S "C2'" "H2'" sing N N 243 T2S "C2'" "H2''" sing N N 244 T2S "C1'" N1 sing N N 245 T2S "C1'" "H1'" sing N N 246 T2S N1 C2 sing N N 247 T2S N1 C6 sing N N 248 T2S C2 O2 doub N N 249 T2S C2 N3 sing N N 250 T2S N3 C4 sing N N 251 T2S N3 H3 sing N N 252 T2S C4 O4 doub N N 253 T2S C4 C5 sing N N 254 T2S C5 C5M sing N N 255 T2S C5 C6 doub N N 256 T2S C5M H71 sing N N 257 T2S C5M H72 sing N N 258 T2S C5M H73 sing N N 259 T2S C6 H6 sing N N 260 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1K8L 'double helix' 1K8L '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 0.459 -0.213 0.198 3.476 -9.454 0.320 1 A_DC1:DG28_B A 1 ? B 28 ? 19 1 1 A DC 2 1_555 B G2S 13 1_555 0.215 -0.199 -0.004 0.468 -11.881 -0.838 2 A_DC2:G2S27_B A 2 ? B 27 ? 19 1 1 A DA 3 1_555 B DT 12 1_555 0.210 -0.069 -0.151 4.025 -1.795 -4.832 3 A_DA3:DT26_B A 3 ? B 26 ? 20 1 1 A DG 4 1_555 B DC 11 1_555 -0.381 -0.208 0.097 8.173 -0.256 -0.672 4 A_DG4:DC25_B A 4 ? B 25 ? 19 1 1 A DG 5 1_555 B C2S 10 1_555 -0.492 -0.260 -0.177 -1.859 -6.693 -0.540 5 A_DG5:C2S24_B A 5 ? B 24 ? 19 1 1 A DA 6 1_555 B DT 9 1_555 0.163 -0.094 -0.159 -5.788 -7.764 -1.340 6 A_DA6:DT23_B A 6 ? B 23 ? 20 1 1 A DG 7 1_555 B C2S 8 1_555 -0.365 -0.218 -0.003 -2.788 -5.687 -1.133 7 A_DG7:C2S22_B A 7 ? B 22 ? 19 1 1 A DA 8 1_555 B DT 7 1_555 0.077 -0.114 -0.208 -0.340 -10.564 -0.130 8 A_DA8:DT21_B A 8 ? B 21 ? 20 1 1 A DT 9 1_555 B DA 6 1_555 -0.090 -0.120 -0.110 -5.511 -10.748 -0.441 9 A_DT9:DA20_B A 9 ? B 20 ? 20 1 1 A T2S 10 1_555 B DA 5 1_555 -0.102 -0.140 -0.452 -0.595 -10.870 -2.384 10 A_T2S10:DA19_B A 10 ? B 19 ? 20 1 1 A C2S 11 1_555 B DG 4 1_555 0.398 -0.221 0.139 -5.916 -2.151 -0.676 11 A_C2S11:DG18_B A 11 ? B 18 ? 19 1 1 A DC 12 1_555 B G2S 3 1_555 0.379 -0.223 0.218 -3.966 0.539 -0.624 12 A_DC12:G2S17_B A 12 ? B 17 ? 19 1 1 A DA 13 1_555 B DT 2 1_555 0.193 -0.106 -0.123 -2.233 -6.055 -1.896 13 A_DA13:DT16_B A 13 ? B 16 ? 20 1 1 A DC 14 1_555 B DG 1 1_555 0.453 -0.227 0.265 -3.382 0.805 -0.164 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 G2S 13 1_555 -0.089 0.129 3.347 3.163 -2.333 41.415 0.433 0.468 3.320 -3.290 -4.461 41.593 1 AA_DC1DC2:G2S27DG28_BB A 1 ? B 28 ? A 2 ? B 27 ? 1 A DC 2 1_555 B G2S 13 1_555 A DA 3 1_555 B DT 12 1_555 -0.934 -0.445 3.174 0.724 14.176 25.926 -3.704 1.979 2.564 28.995 -1.481 29.499 2 AA_DC2DA3:DT26G2S27_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 0.658 -1.430 3.167 -2.970 1.263 28.429 -3.165 -1.970 3.019 2.561 6.023 28.608 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 0.063 -1.282 3.494 1.954 3.701 37.323 -2.499 0.169 3.355 5.761 -3.041 37.548 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 -0.531 -0.863 3.342 -1.376 4.508 38.276 -1.870 0.632 3.240 6.843 2.089 38.555 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 0.647 -1.669 3.169 0.053 6.018 23.568 -5.678 -1.520 2.667 14.434 -0.126 24.314 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 -0.234 -0.418 3.296 0.954 10.709 39.790 -1.745 0.435 3.082 15.396 -1.371 41.160 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 -0.197 -1.334 3.426 -0.297 2.418 25.990 -3.633 0.354 3.292 5.362 0.658 26.102 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 T2S 10 1_555 B DA 5 1_555 0.555 0.047 3.060 6.368 7.114 39.595 -0.682 -0.127 3.072 10.321 -9.238 40.685 9 AA_DT9T2S10:DA19DA20_BB A 9 ? B 20 ? A 10 ? B 19 ? 1 A T2S 10 1_555 B DA 5 1_555 A C2S 11 1_555 B DG 4 1_555 0.364 -1.152 3.457 -3.707 5.935 31.409 -3.162 -1.332 3.130 10.796 6.742 32.160 10 AA_T2S10C2S11:DG18DA19_BB A 10 ? B 19 ? A 11 ? B 18 ? 1 A C2S 11 1_555 B DG 4 1_555 A DC 12 1_555 B G2S 3 1_555 -0.080 -0.941 3.259 -0.386 -0.429 39.634 -1.338 0.073 3.269 -0.633 0.569 39.638 11 AA_C2S11DC12:G2S17DG18_BB A 11 ? B 18 ? A 12 ? B 17 ? 1 A DC 12 1_555 B G2S 3 1_555 A DA 13 1_555 B DT 2 1_555 -0.699 -0.811 3.165 3.091 1.951 31.754 -1.808 1.801 3.032 3.550 -5.626 31.959 12 AA_DC12DA13:DT16G2S17_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 0.234 -0.812 3.412 -5.238 -2.896 40.418 -0.830 -0.939 3.405 -4.164 7.531 40.840 13 AA_DA13DC14:DG15DT16_BB A 13 ? B 16 ? A 14 ? B 15 ? # 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 # _atom_sites.entry_id 1K8L _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_