data_1QDF # _entry.id 1QDF # _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 1QDF pdb_00001qdf 10.2210/pdb1qdf/pdb WWPDB D_1000175906 ? ? # 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 1996-11-08 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 5 'Structure model' 1 4 2024-05-22 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' Other 6 5 'Structure model' 'Data collection' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_site' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1QDF _pdbx_database_status.recvd_initial_deposition_date 1996-04-11 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _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_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1C32 'ENSEMBLE OF 10 STRUCTURES' unspecified PDB 1QDG 'THEORETICAL MODEL' unspecified PDB 1QDH 'MINIMIZED AVERAGE STRUCTURE' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Marathias, V.M.' 1 'Wang, K.Y.' 2 'Kumar, S.' 3 'Swaminathan, S.' 4 'Bolton, P.H.' 5 # _citation.id primary _citation.title ;Determination of the number and location of the manganese binding sites of DNA quadruplexes in solution by EPR and NMR in the presence and absence of thrombin. ; _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 260 _citation.page_first 378 _citation.page_last 394 _citation.year 1996 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 8757801 _citation.pdbx_database_id_DOI 10.1006/jmbi.1996.0408 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Marathias, V.M.' 1 ? primary 'Wang, K.Y.' 2 ? primary 'Kumar, S.' 3 ? primary 'Pham, T.Q.' 4 ? primary 'Swaminathan, S.' 5 ? primary 'Bolton, P.H.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3') ; _entity.formula_weight 4743.051 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DG)(DG)(DT)(DT)(DG)(DG)(DT)(DG)(DT)(DG)(DG)(DT)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can GGTTGGTGTGGTTGG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # 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 DG n 1 3 DT n 1 4 DT n 1 5 DG n 1 6 DG n 1 7 DT n 1 8 DG n 1 9 DT n 1 10 DG n 1 11 DG n 1 12 DT n 1 13 DT n 1 14 DG n 1 15 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 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_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 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DG 11 11 11 DG G A . n A 1 12 DT 12 12 12 DT T A . n A 1 13 DT 13 13 13 DT T A . n A 1 14 DG 14 14 14 DG G A . n A 1 15 DG 15 15 15 DG G A . n # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 X-PLOR refinement . ? 2 X-PLOR phasing . ? 3 # _cell.entry_id 1QDF _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 1QDF _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 1QDF _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 1QDF _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 1QDF _struct.title 'THE NMR STUDY OF DNA QUADRUPLEX STRUCTURE, APTAMER (15MER) DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1QDF _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'QUDRAPLEX DNA, THROMBIN INHIBITOR, MN BINDING DNA, TELOMERE DNA, DNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1QDF _struct_ref.pdbx_db_accession 1QDF _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1QDF _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 15 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1QDF _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 15 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 15 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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 hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DG 6 O6 ? ? A DG 1 A DG 6 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DG 6 N7 ? ? A DG 1 A DG 6 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog3 hydrog ? ? A DG 1 N7 ? ? ? 1_555 A DG 15 N2 ? ? A DG 1 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DG 15 N1 ? ? A DG 1 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DT 4 O4 ? ? A DG 2 A DT 4 1_555 ? ? ? ? ? ? TYPE_27_PAIR ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DT 4 N3 ? ? A DG 2 A DT 4 1_555 ? ? ? ? ? ? TYPE_27_PAIR ? ? ? hydrog7 hydrog ? ? A DG 2 N7 ? ? ? 1_555 A DG 5 N2 ? ? A DG 2 A DG 5 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DG 5 N1 ? ? A DG 2 A DG 5 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DG 14 O6 ? ? A DG 2 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DG 14 N7 ? ? A DG 2 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A DT 4 N3 ? ? ? 1_555 A DT 13 O4 ? ? A DT 4 A DT 13 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog12 hydrog ? ? A DT 4 O4 ? ? ? 1_555 A DT 13 N3 ? ? A DT 4 A DT 13 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog13 hydrog ? ? A DG 5 N7 ? ? ? 1_555 A DG 11 N2 ? ? A DG 5 A DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A DG 5 O6 ? ? ? 1_555 A DG 11 N1 ? ? A DG 5 A DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DG 10 O6 ? ? A DG 6 A DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DG 10 N7 ? ? A DG 6 A DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog17 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DG 15 O6 ? ? A DG 10 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DG 15 N7 ? ? A DG 10 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A DG 11 N1 ? ? ? 1_555 A DT 13 O4 ? ? A DG 11 A DT 13 1_555 ? ? ? ? ? ? TYPE_27_PAIR ? ? ? hydrog20 hydrog ? ? A DG 11 O6 ? ? ? 1_555 A DT 13 N3 ? ? A DG 11 A DT 13 1_555 ? ? ? ? ? ? TYPE_27_PAIR ? ? ? hydrog21 hydrog ? ? A DG 11 N7 ? ? ? 1_555 A DG 14 N2 ? ? A DG 11 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog22 hydrog ? ? A DG 11 O6 ? ? ? 1_555 A DG 14 N1 ? ? A DG 11 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C5 A DT 3 ? ? C7 A DT 3 ? ? 1.532 1.496 0.036 0.006 N 2 1 C5 A DT 7 ? ? C7 A DT 7 ? ? 1.533 1.496 0.037 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 111.72 108.30 3.42 0.30 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.94 108.30 4.64 0.30 N 3 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 111.69 108.30 3.39 0.30 N 4 1 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.11 122.90 -3.79 0.60 N 5 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 114.10 108.30 5.80 0.30 N 6 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 119.23 122.90 -3.67 0.60 N 7 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 111.25 108.30 2.95 0.30 N 8 1 "C3'" A DG 5 ? ? "O3'" A DG 5 ? ? P A DG 6 ? ? 126.94 119.70 7.24 1.20 Y 9 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 113.27 108.30 4.97 0.30 N 10 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 114.35 108.30 6.05 0.30 N 11 1 "C3'" A DT 7 ? ? "O3'" A DT 7 ? ? P A DG 8 ? ? 128.08 119.70 8.38 1.20 Y 12 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.88 108.30 3.58 0.30 N 13 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 113.54 108.30 5.24 0.30 N 14 1 "C3'" A DT 9 ? ? "O3'" A DT 9 ? ? P A DG 10 ? ? 127.73 119.70 8.03 1.20 Y 15 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 113.55 108.30 5.25 0.30 N 16 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 112.25 108.30 3.95 0.30 N 17 1 "O4'" A DT 12 ? ? "C1'" A DT 12 ? ? N1 A DT 12 ? ? 112.46 108.30 4.16 0.30 N 18 1 C6 A DT 12 ? ? C5 A DT 12 ? ? C7 A DT 12 ? ? 119.24 122.90 -3.66 0.60 N 19 1 "O4'" A DT 13 ? ? "C1'" A DT 13 ? ? N1 A DT 13 ? ? 113.92 108.30 5.62 0.30 N 20 1 "O4'" A DG 14 ? ? "C1'" A DG 14 ? ? N9 A DG 14 ? ? 112.51 108.30 4.21 0.30 N 21 1 "C3'" A DG 14 ? ? "O3'" A DG 14 ? ? P A DG 15 ? ? 127.74 119.70 8.04 1.20 Y # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 "C4'" ? A DT 3 ? 'WRONG HAND' . 2 1 "C3'" ? A DT 3 ? 'WRONG HAND' . 3 1 "C1'" ? A DT 3 ? 'WRONG HAND' . 4 1 "C3'" ? A DG 8 ? 'WRONG HAND' . 5 1 "C4'" ? A DT 12 ? 'WRONG HAND' . 6 1 "C3'" ? A DT 12 ? 'WRONG HAND' . 7 1 "C1'" ? A DT 12 ? 'WRONG HAND' . # _pdbx_nmr_ensemble.entry_id 1QDF _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'MINIMIZED AVERAGE' # _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name X-PLOR _pdbx_nmr_software.version ? _pdbx_nmr_software.authors BRUNGER _pdbx_nmr_software.ordinal 1 # 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 DG OP3 O N N 1 DG P P N N 2 DG OP1 O N N 3 DG OP2 O N N 4 DG "O5'" O N N 5 DG "C5'" C N N 6 DG "C4'" C N R 7 DG "O4'" O N N 8 DG "C3'" C N S 9 DG "O3'" O N N 10 DG "C2'" C N N 11 DG "C1'" C N R 12 DG N9 N Y N 13 DG C8 C Y N 14 DG N7 N Y N 15 DG C5 C Y N 16 DG C6 C N N 17 DG O6 O N N 18 DG N1 N N N 19 DG C2 C N N 20 DG N2 N N N 21 DG N3 N N N 22 DG C4 C Y N 23 DG HOP3 H N N 24 DG HOP2 H N N 25 DG "H5'" H N N 26 DG "H5''" H N N 27 DG "H4'" H N N 28 DG "H3'" H N N 29 DG "HO3'" H N N 30 DG "H2'" H N N 31 DG "H2''" H N N 32 DG "H1'" H N N 33 DG H8 H N N 34 DG H1 H N N 35 DG H21 H N N 36 DG H22 H N N 37 DT OP3 O N N 38 DT P P N N 39 DT OP1 O N N 40 DT OP2 O N N 41 DT "O5'" O N N 42 DT "C5'" C N N 43 DT "C4'" C N R 44 DT "O4'" O N N 45 DT "C3'" C N S 46 DT "O3'" O N N 47 DT "C2'" C N N 48 DT "C1'" C N R 49 DT N1 N N N 50 DT C2 C N N 51 DT O2 O N N 52 DT N3 N N N 53 DT C4 C N N 54 DT O4 O N N 55 DT C5 C N N 56 DT C7 C N N 57 DT C6 C N N 58 DT HOP3 H N N 59 DT HOP2 H N N 60 DT "H5'" H N N 61 DT "H5''" H N N 62 DT "H4'" H N N 63 DT "H3'" H N N 64 DT "HO3'" H N N 65 DT "H2'" H N N 66 DT "H2''" H N N 67 DT "H1'" H N N 68 DT H3 H N N 69 DT H71 H N N 70 DT H72 H N N 71 DT H73 H N N 72 DT H6 H N N 73 # 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 DG OP3 P sing N N 1 DG OP3 HOP3 sing N N 2 DG P OP1 doub N N 3 DG P OP2 sing N N 4 DG P "O5'" sing N N 5 DG OP2 HOP2 sing N N 6 DG "O5'" "C5'" sing N N 7 DG "C5'" "C4'" sing N N 8 DG "C5'" "H5'" sing N N 9 DG "C5'" "H5''" sing N N 10 DG "C4'" "O4'" sing N N 11 DG "C4'" "C3'" sing N N 12 DG "C4'" "H4'" sing N N 13 DG "O4'" "C1'" sing N N 14 DG "C3'" "O3'" sing N N 15 DG "C3'" "C2'" sing N N 16 DG "C3'" "H3'" sing N N 17 DG "O3'" "HO3'" sing N N 18 DG "C2'" "C1'" sing N N 19 DG "C2'" "H2'" sing N N 20 DG "C2'" "H2''" sing N N 21 DG "C1'" N9 sing N N 22 DG "C1'" "H1'" sing N N 23 DG N9 C8 sing Y N 24 DG N9 C4 sing Y N 25 DG C8 N7 doub Y N 26 DG C8 H8 sing N N 27 DG N7 C5 sing Y N 28 DG C5 C6 sing N N 29 DG C5 C4 doub Y N 30 DG C6 O6 doub N N 31 DG C6 N1 sing N N 32 DG N1 C2 sing N N 33 DG N1 H1 sing N N 34 DG C2 N2 sing N N 35 DG C2 N3 doub N N 36 DG N2 H21 sing N N 37 DG N2 H22 sing N N 38 DG N3 C4 sing N N 39 DT OP3 P sing N N 40 DT OP3 HOP3 sing N N 41 DT P OP1 doub N N 42 DT P OP2 sing N N 43 DT P "O5'" sing N N 44 DT OP2 HOP2 sing N N 45 DT "O5'" "C5'" sing N N 46 DT "C5'" "C4'" sing N N 47 DT "C5'" "H5'" sing N N 48 DT "C5'" "H5''" sing N N 49 DT "C4'" "O4'" sing N N 50 DT "C4'" "C3'" sing N N 51 DT "C4'" "H4'" sing N N 52 DT "O4'" "C1'" sing N N 53 DT "C3'" "O3'" sing N N 54 DT "C3'" "C2'" sing N N 55 DT "C3'" "H3'" sing N N 56 DT "O3'" "HO3'" sing N N 57 DT "C2'" "C1'" sing N N 58 DT "C2'" "H2'" sing N N 59 DT "C2'" "H2''" sing N N 60 DT "C1'" N1 sing N N 61 DT "C1'" "H1'" sing N N 62 DT N1 C2 sing N N 63 DT N1 C6 sing N N 64 DT C2 O2 doub N N 65 DT C2 N3 sing N N 66 DT N3 C4 sing N N 67 DT N3 H3 sing N N 68 DT C4 O4 doub N N 69 DT C4 C5 sing N N 70 DT C5 C7 sing N N 71 DT C5 C6 doub N N 72 DT C7 H71 sing N N 73 DT C7 H72 sing N N 74 DT C7 H73 sing N N 75 DT C6 H6 sing N N 76 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1QDF 'double helix' 1QDF 'quadruple 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 DT 4 1_555 A DT 13 1_555 1.509 -1.827 -0.154 18.763 -30.810 175.733 1 A_DT4:DT13_A A 4 ? A 13 ? 12 2 1 A DG 5 1_555 A DG 11 1_555 -2.275 -3.043 -0.089 6.526 -8.662 86.932 2 A_DG5:DG11_A A 5 ? A 11 ? 6 ? 1 A DG 2 1_555 A DG 14 1_555 2.172 3.123 -0.068 -9.316 3.678 -85.954 3 A_DG2:DG14_A A 2 ? A 14 ? 6 ? 1 A DG 6 1_555 A DG 10 1_555 1.896 3.236 -0.094 13.568 -9.813 -86.436 4 A_DG6:DG10_A A 6 ? A 10 ? 6 ? 1 A DG 1 1_555 A DG 15 1_555 -1.808 -3.196 0.138 9.749 15.023 88.576 5 A_DG1:DG15_A A 1 ? A 15 ? 6 ? # 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 DT 4 1_555 A DT 13 1_555 A DG 5 1_555 A DG 11 1_555 -1.950 1.405 1.316 153.353 90.088 38.254 0.553 1.230 -0.484 45.409 -77.298 177.975 1 AA_DT4DG5:DG11DT13_AA A 4 ? A 13 ? A 5 ? A 11 ? 1 A DG 5 1_555 A DG 11 1_555 A DG 2 1_555 A DG 14 1_555 -1.069 -3.563 -0.344 1.936 -1.088 179.720 -1.782 0.535 -0.344 -0.544 -0.968 179.720 2 AA_DG5DG2:DG14DG11_AA A 5 ? A 11 ? A 2 ? A 14 ? 1 A DG 2 1_555 A DG 14 1_555 A DG 6 1_555 A DG 10 1_555 -0.093 2.869 -1.756 -153.791 -77.455 -62.604 -1.644 0.365 0.117 39.570 -78.568 -173.332 3 AA_DG2DG6:DG10DG14_AA A 2 ? A 14 ? A 6 ? A 10 ? 1 A DG 6 1_555 A DG 10 1_555 A DG 1 1_555 A DG 15 1_555 1.822 3.137 0.038 16.072 -13.877 -179.931 -1.569 0.911 0.038 6.938 8.036 -179.933 4 AA_DG6DG1:DG15DG10_AA A 6 ? A 10 ? A 1 ? A 15 ? # _atom_sites.entry_id 1QDF _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_