data_105D # _entry.id 105D # _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 105D pdb_0000105d 10.2210/pdb105d/pdb WWPDB D_1000170013 ? ? # 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 1995-02-07 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 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 105D _pdbx_database_status.recvd_initial_deposition_date 1994-12-22 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Leroy, J.-L.' 1 'Gueron, M.' 2 # _citation.id primary _citation.title ;Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons. ; _citation.journal_abbrev Structure _citation.journal_volume 3 _citation.page_first 101 _citation.page_last 120 _citation.year 1995 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 7743125 _citation.pdbx_database_id_DOI '10.1016/S0969-2126(01)00138-1' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Leroy, J.L.' 1 ? primary 'Gueron, M.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*TP*CP*C)-3') ; _entity.formula_weight 837.599 _entity.pdbx_number_of_molecules 4 _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 '(DT)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can TCC _entity_poly.pdbx_strand_id A,B,C,D _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 DT n 1 2 DC n 1 3 DC 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 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 DT 1 1 1 DT T A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DC 3 3 3 DC C A . n B 1 1 DT 1 4 4 DT T B . n B 1 2 DC 2 5 5 DC C B . n B 1 3 DC 3 6 6 DC C B . n C 1 1 DT 1 7 7 DT T C . n C 1 2 DC 2 8 8 DC C C . n C 1 3 DC 3 9 9 DC C C . n D 1 1 DT 1 10 10 DT T D . n D 1 2 DC 2 11 11 DC C D . n D 1 3 DC 3 12 12 DC C D . 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 105D _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 105D _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 105D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 105D _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 105D _struct.title ;SOLUTION STRUCTURES OF THE I-MOTIF TETRAMERS OF D(TCC), D(5MCCT) AND D(T5MCC). NOVEL NOE CONNECTIONS BETWEEN AMINO PROTONS AND SUGAR PROTONS ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 105D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 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 ? C N N 1 ? D N N 1 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 105D _struct_ref.pdbx_db_accession 105D _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 105D A 1 ? 3 ? 105D 1 ? 3 ? 1 3 2 1 105D B 1 ? 3 ? 105D 4 ? 6 ? 4 6 3 1 105D C 1 ? 3 ? 105D 7 ? 9 ? 7 9 4 1 105D D 1 ? 3 ? 105D 10 ? 12 ? 10 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 2 N4 ? ? ? 1_555 C DC 2 O2 ? ? A DC 2 C DC 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog2 hydrog ? ? A DC 2 O2 ? ? ? 1_555 C DC 2 N4 ? ? A DC 2 C DC 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog3 hydrog ? ? A DC 3 N4 ? ? ? 1_555 C DC 3 O2 ? ? A DC 3 C DC 9 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog4 hydrog ? ? A DC 3 O2 ? ? ? 1_555 C DC 3 N4 ? ? A DC 3 C DC 9 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog5 hydrog ? ? B DC 2 N4 ? ? ? 1_555 D DC 2 O2 ? ? B DC 5 D DC 11 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog6 hydrog ? ? B DC 2 O2 ? ? ? 1_555 D DC 2 N4 ? ? B DC 5 D DC 11 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog7 hydrog ? ? B DC 3 N4 ? ? ? 1_555 D DC 3 O2 ? ? B DC 6 D DC 12 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog8 hydrog ? ? B DC 3 O2 ? ? ? 1_555 D DC 3 N4 ? ? B DC 6 D DC 12 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.75 108.30 2.45 0.30 N 2 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.09 108.30 2.79 0.30 N 3 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.75 108.30 2.45 0.30 N 4 1 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 110.80 108.30 2.50 0.30 N 5 1 C6 B DT 4 ? ? C5 B DT 4 ? ? C7 B DT 4 ? ? 119.23 122.90 -3.67 0.60 N 6 1 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 112.37 108.30 4.07 0.30 N 7 1 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.74 108.30 2.44 0.30 N 8 1 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 111.46 108.30 3.16 0.30 N 9 1 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 111.00 108.30 2.70 0.30 N 10 1 "O4'" C DC 9 ? ? "C1'" C DC 9 ? ? N1 C DC 9 ? ? 110.42 108.30 2.12 0.30 N 11 1 "O4'" D DT 10 ? ? "C1'" D DT 10 ? ? N1 D DT 10 ? ? 110.93 108.30 2.63 0.30 N 12 1 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.06 108.30 2.76 0.30 N 13 1 "O4'" D DC 12 ? ? "C1'" D DC 12 ? ? N1 D DC 12 ? ? 110.36 108.30 2.06 0.30 N 14 2 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.83 108.30 2.53 0.30 N 15 2 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 112.51 108.30 4.21 0.30 N 16 2 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.44 108.30 2.14 0.30 N 17 2 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 110.96 108.30 2.66 0.30 N 18 2 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 112.52 108.30 4.22 0.30 N 19 2 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.36 108.30 2.06 0.30 N 20 2 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 110.86 108.30 2.56 0.30 N 21 2 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 111.12 108.30 2.82 0.30 N 22 2 "O4'" C DC 9 ? ? "C1'" C DC 9 ? ? N1 C DC 9 ? ? 110.79 108.30 2.49 0.30 N 23 2 "O4'" D DT 10 ? ? "C1'" D DT 10 ? ? N1 D DT 10 ? ? 110.75 108.30 2.45 0.30 N 24 2 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.96 108.30 3.66 0.30 N 25 2 "O4'" D DC 12 ? ? "C1'" D DC 12 ? ? N1 D DC 12 ? ? 110.39 108.30 2.09 0.30 N 26 3 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.84 108.30 2.54 0.30 N 27 3 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.88 108.30 3.58 0.30 N 28 3 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.30 108.30 2.00 0.30 N 29 3 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 111.35 108.30 3.05 0.30 N 30 3 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 111.18 108.30 2.88 0.30 N 31 3 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.79 108.30 2.49 0.30 N 32 3 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 110.65 108.30 2.35 0.30 N 33 3 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 111.18 108.30 2.88 0.30 N 34 3 "O4'" C DC 9 ? ? "C1'" C DC 9 ? ? N1 C DC 9 ? ? 110.96 108.30 2.66 0.30 N 35 3 "O4'" D DT 10 ? ? "C1'" D DT 10 ? ? N1 D DT 10 ? ? 111.12 108.30 2.82 0.30 N 36 3 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.71 108.30 3.41 0.30 N 37 3 "O4'" D DC 12 ? ? "C1'" D DC 12 ? ? N1 D DC 12 ? ? 110.42 108.30 2.12 0.30 N 38 4 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 111.06 108.30 2.76 0.30 N 39 4 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.03 108.30 2.73 0.30 N 40 4 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.54 108.30 2.24 0.30 N 41 4 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 111.53 108.30 3.23 0.30 N 42 4 C6 B DT 4 ? ? C5 B DT 4 ? ? C7 B DT 4 ? ? 119.28 122.90 -3.62 0.60 N 43 4 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.97 108.30 2.67 0.30 N 44 4 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 111.10 108.30 2.80 0.30 N 45 4 C6 C DT 7 ? ? C5 C DT 7 ? ? C7 C DT 7 ? ? 119.28 122.90 -3.62 0.60 N 46 4 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 111.03 108.30 2.73 0.30 N 47 4 "O4'" C DC 9 ? ? "C1'" C DC 9 ? ? N1 C DC 9 ? ? 110.84 108.30 2.54 0.30 N 48 4 "O4'" D DT 10 ? ? "C1'" D DT 10 ? ? N1 D DT 10 ? ? 110.67 108.30 2.37 0.30 N 49 4 C6 D DT 10 ? ? C5 D DT 10 ? ? C7 D DT 10 ? ? 119.28 122.90 -3.62 0.60 N 50 4 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.07 108.30 2.77 0.30 N 51 4 "O4'" D DC 12 ? ? "C1'" D DC 12 ? ? N1 D DC 12 ? ? 110.62 108.30 2.32 0.30 N 52 5 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.80 108.30 2.50 0.30 N 53 5 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.49 108.30 3.19 0.30 N 54 5 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.62 108.30 2.32 0.30 N 55 5 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 110.75 108.30 2.45 0.30 N 56 5 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.87 108.30 2.57 0.30 N 57 5 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.78 108.30 2.48 0.30 N 58 5 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 111.73 108.30 3.43 0.30 N 59 5 C6 C DT 7 ? ? C5 C DT 7 ? ? C7 C DT 7 ? ? 119.28 122.90 -3.62 0.60 N 60 5 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.75 108.30 2.45 0.30 N 61 5 "O4'" C DC 9 ? ? "C1'" C DC 9 ? ? N1 C DC 9 ? ? 110.54 108.30 2.24 0.30 N 62 5 "O4'" D DT 10 ? ? "C1'" D DT 10 ? ? N1 D DT 10 ? ? 110.84 108.30 2.54 0.30 N 63 5 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.07 108.30 2.77 0.30 N 64 6 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.98 108.30 2.68 0.30 N 65 6 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.21 108.30 2.91 0.30 N 66 6 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.39 108.30 2.09 0.30 N 67 6 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 110.71 108.30 2.41 0.30 N 68 6 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.99 108.30 2.69 0.30 N 69 6 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.44 108.30 2.14 0.30 N 70 6 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 110.80 108.30 2.50 0.30 N 71 6 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.88 108.30 2.58 0.30 N 72 6 "O4'" C DC 9 ? ? "C1'" C DC 9 ? ? N1 C DC 9 ? ? 110.55 108.30 2.25 0.30 N 73 6 "O4'" D DT 10 ? ? "C1'" D DT 10 ? ? N1 D DT 10 ? ? 110.64 108.30 2.34 0.30 N 74 6 C6 D DT 10 ? ? C5 D DT 10 ? ? C7 D DT 10 ? ? 119.30 122.90 -3.60 0.60 N 75 6 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.01 108.30 2.71 0.30 N 76 6 "O4'" D DC 12 ? ? "C1'" D DC 12 ? ? N1 D DC 12 ? ? 110.73 108.30 2.43 0.30 N 77 7 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.69 108.30 2.39 0.30 N 78 7 C6 A DT 1 ? ? C5 A DT 1 ? ? C7 A DT 1 ? ? 119.26 122.90 -3.64 0.60 N 79 7 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.22 108.30 2.92 0.30 N 80 7 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.26 108.30 1.96 0.30 N 81 7 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 110.78 108.30 2.48 0.30 N 82 7 C6 B DT 4 ? ? C5 B DT 4 ? ? C7 B DT 4 ? ? 119.27 122.90 -3.63 0.60 N 83 7 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.70 108.30 2.40 0.30 N 84 7 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.32 108.30 2.02 0.30 N 85 7 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 111.43 108.30 3.13 0.30 N 86 7 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 111.19 108.30 2.89 0.30 N 87 7 "O4'" C DC 9 ? ? "C1'" C DC 9 ? ? N1 C DC 9 ? ? 110.35 108.30 2.05 0.30 N 88 7 "O4'" D DT 10 ? ? "C1'" D DT 10 ? ? N1 D DT 10 ? ? 110.81 108.30 2.51 0.30 N 89 7 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 110.80 108.30 2.50 0.30 N 90 7 "O4'" D DC 12 ? ? "C1'" D DC 12 ? ? N1 D DC 12 ? ? 110.48 108.30 2.18 0.30 N 91 8 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.91 108.30 2.61 0.30 N 92 8 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.96 108.30 3.66 0.30 N 93 8 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.49 108.30 2.19 0.30 N 94 8 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 110.79 108.30 2.49 0.30 N 95 8 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 111.36 108.30 3.06 0.30 N 96 8 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.85 108.30 2.55 0.30 N 97 8 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 110.62 108.30 2.32 0.30 N 98 8 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 111.39 108.30 3.09 0.30 N 99 8 "O4'" C DC 9 ? ? "C1'" C DC 9 ? ? N1 C DC 9 ? ? 110.74 108.30 2.44 0.30 N 100 8 "O4'" D DT 10 ? ? "C1'" D DT 10 ? ? N1 D DT 10 ? ? 111.29 108.30 2.99 0.30 N 101 8 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 112.09 108.30 3.79 0.30 N 102 8 "O4'" D DC 12 ? ? "C1'" D DC 12 ? ? N1 D DC 12 ? ? 111.20 108.30 2.90 0.30 N # _pdbx_nmr_ensemble.entry_id 105D _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 8 _pdbx_nmr_ensemble.conformer_selection_criteria ? _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_refine.entry_id 105D _pdbx_nmr_refine.method ? _pdbx_nmr_refine.details ;THE STRUCTURE IS FORMED OF FOUR EQUIVALENT TCC STRANDS DESIGNATED A, B, C, D. STRANDS A AND C, CONNECTED BY TWO HEMI-PROTONATED BASE PAIRS (C2.C2+ AND C3.C3+), FORM A PARALLEL-STRANDED DUPLEX. THE RELATION BETWEEN STRANDS B AND D IS THE SAME AS THAT BETWEEN STRANDS A AND C. THE STRANDS OF EACH DUPLEX ARE RELATED BY A LONGITUDINAL TWO-FOLD SYMMETRY AXIS. THE DUPLEXES HAVE THE SAME LONGITUDINAL AXIS, AND THEY ARE ANTI-PARALLEL. THEIR HEMI-PROTONATED C.C+ BASE PAIRS ARE INTERCALATED FACE-TO-FACE. THE DUPLEXES CAN BE TRANSFORMED INTO ONE ANOTHER BY A 180 DEGREE ROTATION AROUND A TWO-FOLD AXIS PERPENDICULAR TO THE LONGITUDINAL AXIS, AND CONSEQUENTLY AROUND A THIRD AXIS PERPENDICULAR TO THE FIRST TWO. THE H3 IMINO PROTONS OF THE HEMI-PROTONATED C.C+ PAIRS WERE NOT INCORPORATED IN THE COMPUTATIONS. ; _pdbx_nmr_refine.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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DT OP3 O N N 35 DT P P N N 36 DT OP1 O N N 37 DT OP2 O N N 38 DT "O5'" O N N 39 DT "C5'" C N N 40 DT "C4'" C N R 41 DT "O4'" O N N 42 DT "C3'" C N S 43 DT "O3'" O N N 44 DT "C2'" C N N 45 DT "C1'" C N R 46 DT N1 N N N 47 DT C2 C N N 48 DT O2 O N N 49 DT N3 N N N 50 DT C4 C N N 51 DT O4 O N N 52 DT C5 C N N 53 DT C7 C N N 54 DT C6 C N N 55 DT HOP3 H N N 56 DT HOP2 H N N 57 DT "H5'" H N N 58 DT "H5''" H N N 59 DT "H4'" H N N 60 DT "H3'" H N N 61 DT "HO3'" H N N 62 DT "H2'" H N N 63 DT "H2''" H N N 64 DT "H1'" H N N 65 DT H3 H N N 66 DT H71 H N N 67 DT H72 H N N 68 DT H73 H N N 69 DT H6 H N N 70 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DT OP3 P sing N N 36 DT OP3 HOP3 sing N N 37 DT P OP1 doub N N 38 DT P OP2 sing N N 39 DT P "O5'" sing N N 40 DT OP2 HOP2 sing N N 41 DT "O5'" "C5'" sing N N 42 DT "C5'" "C4'" sing N N 43 DT "C5'" "H5'" sing N N 44 DT "C5'" "H5''" sing N N 45 DT "C4'" "O4'" sing N N 46 DT "C4'" "C3'" sing N N 47 DT "C4'" "H4'" sing N N 48 DT "O4'" "C1'" sing N N 49 DT "C3'" "O3'" sing N N 50 DT "C3'" "C2'" sing N N 51 DT "C3'" "H3'" sing N N 52 DT "O3'" "HO3'" sing N N 53 DT "C2'" "C1'" sing N N 54 DT "C2'" "H2'" sing N N 55 DT "C2'" "H2''" sing N N 56 DT "C1'" N1 sing N N 57 DT "C1'" "H1'" sing N N 58 DT N1 C2 sing N N 59 DT N1 C6 sing N N 60 DT C2 O2 doub N N 61 DT C2 N3 sing N N 62 DT N3 C4 sing N N 63 DT N3 H3 sing N N 64 DT C4 O4 doub N N 65 DT C4 C5 sing N N 66 DT C5 C7 sing N N 67 DT C5 C6 doub N N 68 DT C7 H71 sing N N 69 DT C7 H72 sing N N 70 DT C7 H73 sing N N 71 DT C6 H6 sing N N 72 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 105D 'double helix' 105D 'parallel strands' # 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 3 1_555 C DC 3 1_555 2.213 2.016 -0.059 3.222 4.377 179.967 1 A_DC3:DC9_C A 3 ? C 9 ? 15 2 1 D DC 2 1_555 B DC 2 1_555 2.114 1.795 0.208 3.331 -5.387 179.359 2 D_DC11:DC5_B D 11 ? B 5 ? 15 2 1 A DC 2 1_555 C DC 2 1_555 -1.993 -1.622 0.114 10.796 8.801 -179.892 3 A_DC2:DC8_C A 2 ? C 8 ? 15 2 1 D DC 3 1_555 B DC 3 1_555 -2.343 -2.069 -0.383 -13.245 -2.243 -177.187 4 D_DC12:DC6_B D 12 ? B 6 ? 15 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 A DC 3 1_555 C DC 3 1_555 D DC 2 1_555 B DC 2 1_555 1.200 -2.918 0.369 151.676 90.232 -94.241 1.364 0.761 0.584 -45.356 76.241 -177.610 1 AD_DC3DC11:DC5DC9_BC A 3 ? C 9 ? D 11 ? B 5 ? 1 D DC 2 1_555 B DC 2 1_555 A DC 2 1_555 C DC 2 1_555 1.856 2.134 -0.079 123.318 -127.854 -35.689 -1.033 0.962 0.211 64.517 62.229 -177.748 2 DA_DC11DC2:DC8DC5_CB D 11 ? B 5 ? A 2 ? C 8 ? 1 A DC 2 1_555 C DC 2 1_555 D DC 3 1_555 B DC 3 1_555 1.483 -2.901 -0.175 153.081 86.075 -68.834 1.473 0.703 0.008 -43.504 77.370 -176.388 3 AD_DC2DC12:DC6DC8_BC A 2 ? C 8 ? D 12 ? B 6 ? # _atom_sites.entry_id 105D _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_