data_1QDI # _entry.id 1QDI # _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 1QDI pdb_00001qdi 10.2210/pdb1qdi/pdb WWPDB D_1000175909 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1QDJ 'THEORETICAL MODEL' unspecified PDB 1QDK 'MINIMIZED AVERAGE STRUCTURE' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1QDI _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_ _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 ? # _cell.entry_id 1QDI _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 1QDI _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3') ; _entity.formula_weight 3805.460 _entity.pdbx_number_of_molecules 2 _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)(DG)(DG)(DT)(DT)(DT)(DT)(DG)(DG)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can GGGGTTTTGGGG _entity_poly.pdbx_strand_id A,B _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 DG n 1 4 DG n 1 5 DT n 1 6 DT n 1 7 DT n 1 8 DT n 1 9 DG n 1 10 DG n 1 11 DG n 1 12 DG n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1QDI _struct_ref.pdbx_db_accession 1QDI _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1QDI A 1 ? 12 ? 1QDI 1 ? 12 ? 1 12 2 1 1QDI B 1 ? 12 ? 1QDI 1 ? 12 ? 1 12 # 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 # _pdbx_nmr_ensemble.entry_id 1QDI _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 # _exptl.entry_id 1QDI _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1QDI _struct.title 'THE NMR STUDY OF DNA QUADRUPLEX STRUCTURE, (12MER) DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1QDI _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'QUDRAPLEX DNA, MN BINDING DNA, NON-THROMBIN INHIBITOR, TELOMERE DNA DUPLEX, 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 1 ? # _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 N7 ? ? ? 1_555 B DG 4 N2 ? ? A DG 1 B DG 4 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog2 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DG 4 N1 ? ? A DG 1 B DG 4 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog3 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DG 9 O6 ? ? A DG 1 B DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DG 9 N7 ? ? A DG 1 B DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DG 10 O6 ? ? A DG 1 B DG 10 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog6 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DG 3 O6 ? ? A DG 2 B DG 3 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DG 3 N7 ? ? A DG 2 B DG 3 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 2 N7 ? ? ? 1_555 B DG 10 N2 ? ? A DG 2 B DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DG 10 N1 ? ? A DG 2 B DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A DG 3 N7 ? ? ? 1_555 B DG 2 N2 ? ? A DG 3 B DG 2 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DG 2 N1 ? ? A DG 3 B DG 2 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DG 11 O6 ? ? A DG 3 B DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DG 11 N7 ? ? A DG 3 B DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DG 1 O6 ? ? A DG 4 B DG 1 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DG 1 N7 ? ? A DG 4 B DG 1 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A DG 4 N7 ? ? ? 1_555 B DG 12 N2 ? ? A DG 4 B DG 12 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog17 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DG 12 N1 ? ? A DG 4 B DG 12 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A DT 5 N3 ? ? ? 1_555 A DT 7 O2 ? ? A DT 5 A DT 7 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog19 hydrog ? ? A DT 5 O2 ? ? ? 1_555 A DT 7 N3 ? ? A DT 5 A DT 7 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog20 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DG 1 O6 ? ? A DT 5 B DG 1 1_555 ? ? ? ? ? ? 'DT-DG MISPAIR' ? ? ? hydrog21 hydrog ? ? A DG 9 N7 ? ? ? 1_555 B DG 1 N2 ? ? A DG 9 B DG 1 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog22 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DG 1 N1 ? ? A DG 9 B DG 1 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog23 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DG 12 O6 ? ? A DG 9 B DG 12 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog24 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DG 12 N7 ? ? A DG 9 B DG 12 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog25 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DG 2 O6 ? ? A DG 10 B DG 2 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog26 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DG 2 N7 ? ? A DG 10 B DG 2 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog27 hydrog ? ? A DG 10 N7 ? ? ? 1_555 B DG 11 N2 ? ? A DG 10 B DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog28 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DG 11 N1 ? ? A DG 10 B DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog29 hydrog ? ? A DG 11 N7 ? ? ? 1_555 B DG 3 N2 ? ? A DG 11 B DG 3 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog30 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DG 3 N1 ? ? A DG 11 B DG 3 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog31 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DG 10 O6 ? ? A DG 11 B DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog32 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DG 10 N7 ? ? A DG 11 B DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog33 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DG 4 O6 ? ? A DG 12 B DG 4 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog34 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DG 4 N7 ? ? A DG 12 B DG 4 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog35 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DT 5 O4 ? ? A DG 12 B DT 5 1_555 ? ? ? ? ? ? 'DG-DT MISPAIR' ? ? ? hydrog36 hydrog ? ? A DG 12 N7 ? ? ? 1_555 B DG 9 N2 ? ? A DG 12 B DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog37 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DG 9 N1 ? ? A DG 12 B DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog38 hydrog ? ? B DT 5 N3 ? ? ? 1_555 B DT 7 O2 ? ? B DT 5 B DT 7 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog39 hydrog ? ? B DT 5 O2 ? ? ? 1_555 B DT 7 N3 ? ? B DT 5 B DT 7 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog40 hydrog ? ? B DT 6 N3 ? ? ? 1_555 B DT 8 O4 ? ? B DT 6 B DT 8 1_555 ? ? ? ? ? ? 'DT-DT MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1QDI _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 1QDI _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DG 9 9 9 DG G 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 DG 12 12 12 DG G A . n B 1 1 DG 1 1 1 DG G B . n B 1 2 DG 2 2 2 DG G B . n B 1 3 DG 3 3 3 DG G B . n B 1 4 DG 4 4 4 DG G B . n B 1 5 DT 5 5 5 DT T B . n B 1 6 DT 6 6 6 DT T B . n B 1 7 DT 7 7 7 DT T B . n B 1 8 DT 8 8 8 DT T B . n B 1 9 DG 9 9 9 DG G B . n B 1 10 DG 10 10 10 DG G B . n B 1 11 DG 11 11 11 DG G B . n B 1 12 DG 12 12 12 DG G B . n # _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 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 # _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 # 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 # 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' # 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 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O2 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 DT _pdbx_validate_close_contact.auth_seq_id_1 5 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 H3 _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 DT _pdbx_validate_close_contact.auth_seq_id_2 7 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.53 # 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 5 ? ? C7 A DT 5 ? ? 1.535 1.496 0.039 0.006 N 2 1 C5 A DT 6 ? ? C7 A DT 6 ? ? 1.533 1.496 0.037 0.006 N 3 1 C5 A DT 7 ? ? C7 A DT 7 ? ? 1.533 1.496 0.037 0.006 N 4 1 C5 A DT 8 ? ? C7 A DT 8 ? ? 1.535 1.496 0.039 0.006 N 5 1 C5 B DT 5 ? ? C7 B DT 5 ? ? 1.538 1.496 0.042 0.006 N 6 1 C5 B DT 6 ? ? C7 B DT 6 ? ? 1.533 1.496 0.037 0.006 N 7 1 C5 B DT 7 ? ? C7 B DT 7 ? ? 1.532 1.496 0.036 0.006 N 8 1 C5 B DT 8 ? ? C7 B DT 8 ? ? 1.535 1.496 0.039 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 ? ? 113.30 108.30 5.00 0.30 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 110.19 108.30 1.89 0.30 N 3 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 113.27 108.30 4.97 0.30 N 4 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 113.14 108.30 4.84 0.30 N 5 1 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 111.62 108.30 3.32 0.30 N 6 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 111.17 108.30 2.87 0.30 N 7 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 118.79 122.90 -4.11 0.60 N 8 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 110.11 108.30 1.81 0.30 N 9 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 112.56 108.30 4.26 0.30 N 10 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 113.20 108.30 4.90 0.30 N 11 1 "C3'" A DG 10 ? ? "O3'" A DG 10 ? ? P A DG 11 ? ? 127.31 119.70 7.61 1.20 Y 12 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 113.35 108.30 5.05 0.30 N 13 1 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 111.98 108.30 3.68 0.30 N 14 1 "O4'" B DG 1 ? ? "C1'" B DG 1 ? ? N9 B DG 1 ? ? 114.45 108.30 6.15 0.30 N 15 1 "O4'" B DG 3 ? ? "C1'" B DG 3 ? ? N9 B DG 3 ? ? 111.37 108.30 3.07 0.30 N 16 1 "O4'" B DG 4 ? ? "C1'" B DG 4 ? ? N9 B DG 4 ? ? 110.40 108.30 2.10 0.30 N 17 1 "O4'" B DT 5 ? ? "C1'" B DT 5 ? ? N1 B DT 5 ? ? 113.79 108.30 5.49 0.30 N 18 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 111.58 108.30 3.28 0.30 N 19 1 C6 B DT 7 ? ? C5 B DT 7 ? ? C7 B DT 7 ? ? 119.04 122.90 -3.86 0.60 N 20 1 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? N1 B DT 8 ? ? 110.20 108.30 1.90 0.30 N 21 1 "O4'" B DG 9 ? ? "C1'" B DG 9 ? ? N9 B DG 9 ? ? 113.92 108.30 5.62 0.30 N 22 1 "C3'" B DG 9 ? ? "O3'" B DG 9 ? ? P B DG 10 ? ? 127.60 119.70 7.90 1.20 Y 23 1 "O4'" B DG 10 ? ? "C1'" B DG 10 ? ? N9 B DG 10 ? ? 113.78 108.30 5.48 0.30 N 24 1 "O4'" B DG 11 ? ? "C1'" B DG 11 ? ? N9 B DG 11 ? ? 114.61 108.30 6.31 0.30 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1QDI 'double helix' 1QDI 'parallel strands' 1QDI '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 B DT 8 1_555 B DT 6 1_555 -1.815 -1.560 0.053 40.911 1.474 44.553 1 B_DT8:DT6_B B 8 ? B 6 ? ? ? 1 B DT 5 1_555 B DT 7 1_555 -2.052 -3.956 -0.366 -2.666 -47.697 -162.614 2 B_DT5:DT7_B B 5 ? B 7 ? 13 2 1 A DG 1 1_555 B DG 4 1_555 -1.296 -3.194 0.203 -21.707 20.239 98.926 3 A_DG1:DG4_B A 1 ? B 4 ? 6 ? 1 A DG 11 1_555 B DG 3 1_555 -1.672 -3.116 -0.288 5.748 8.681 99.467 4 A_DG11:DG3_B A 11 ? B 3 ? 6 ? 1 B DG 2 1_555 A DG 10 1_555 -1.470 -3.285 0.592 -14.316 3.219 93.082 5 B_DG2:DG10_A B 2 ? A 10 ? 6 ? 1 A DG 4 1_555 B DG 12 1_555 -1.765 -3.066 1.083 -13.605 28.667 87.386 6 A_DG4:DG12_B A 4 ? B 12 ? 6 ? 1 B DG 1 1_555 A DG 9 1_555 2.043 2.869 0.381 -0.224 -17.523 -89.168 7 B_DG1:DG9_A B 1 ? A 9 ? 6 ? 1 A DT 5 1_555 A DT 7 1_555 -1.965 -4.016 -0.248 -7.581 -33.064 -157.037 8 A_DT5:DT7_A A 5 ? A 7 ? 13 2 # 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 B DT 8 1_555 B DT 6 1_555 B DT 5 1_555 B DT 7 1_555 -2.495 3.908 -4.720 -33.840 27.348 -42.498 -1.096 0.981 -6.450 -30.016 -37.141 -60.090 1 BB_DT8DT5:DT7DT6_BB B 8 ? B 6 ? B 5 ? B 7 ? 1 B DT 5 1_555 B DT 7 1_555 A DG 1 1_555 B DG 4 1_555 -1.948 -0.055 -2.026 -4.625 9.563 -60.622 0.342 -1.767 -2.126 -9.396 -4.544 -61.458 2 BA_DT5DG1:DG4DT7_BB B 5 ? B 7 ? A 1 ? B 4 ? 1 A DG 1 1_555 B DG 4 1_555 A DG 11 1_555 B DG 3 1_555 -2.664 -1.140 -1.162 -48.018 -165.424 123.795 -0.729 1.379 -0.162 -83.149 24.136 176.353 3 AA_DG1DG11:DG3DG4_BB A 1 ? B 4 ? A 11 ? B 3 ? 1 A DG 11 1_555 B DG 3 1_555 B DG 2 1_555 A DG 10 1_555 -1.485 -2.975 -1.143 -142.128 97.618 -1.407 1.686 -0.460 0.446 -50.928 -74.148 -172.423 4 AB_DG11DG2:DG10DG3_AB A 11 ? B 3 ? B 2 ? A 10 ? 1 B DG 2 1_555 A DG 10 1_555 A DG 4 1_555 B DG 12 1_555 -2.428 1.330 -1.924 -137.650 -62.232 37.753 0.535 1.579 0.929 -35.111 77.660 152.651 5 BA_DG2DG4:DG12DG10_BA B 2 ? A 10 ? A 4 ? B 12 ? 1 A DG 4 1_555 B DG 12 1_555 B DG 1 1_555 A DG 9 1_555 1.998 2.692 1.163 2.599 -20.974 -178.144 -1.345 0.999 1.170 10.488 1.299 -178.176 6 AB_DG4DG1:DG9DG12_AB A 4 ? B 12 ? B 1 ? A 9 ? 1 B DG 1 1_555 A DG 9 1_555 A DT 5 1_555 A DT 7 1_555 2.451 0.930 1.863 16.259 -16.235 -21.791 -0.396 5.821 0.520 33.264 33.313 -31.566 7 BA_DG1DT5:DT7DG9_AA B 1 ? A 9 ? A 5 ? A 7 ? #