data_106D # _entry.id 106D # _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 106D pdb_0000106d 10.2210/pdb106d/pdb WWPDB D_1000170015 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 106D _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 ? # _cell.entry_id 106D _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 106D _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(*MCYP*CP*T)-3') ; _entity.formula_weight 771.646 _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 yes _entity_poly.pdbx_seq_one_letter_code '(MCY)(DC)(DT)' _entity_poly.pdbx_seq_one_letter_code_can CCT _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 MCY n 1 2 DC n 1 3 DT n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 106D _struct_ref.pdbx_db_accession 106D _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 106D A 1 ? 3 ? 106D 1 ? 3 ? 1 3 2 1 106D B 1 ? 3 ? 106D 4 ? 6 ? 4 6 3 1 106D C 1 ? 3 ? 106D 7 ? 9 ? 7 9 4 1 106D D 1 ? 3 ? 106D 10 ? 12 ? 10 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 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 MCY 'DNA linking' n "5-METHYL-2'-DEOXYCYTIDINE" ? 'C10 H15 N3 O4' 241.244 # _pdbx_nmr_refine.entry_id 106D _pdbx_nmr_refine.method ? _pdbx_nmr_refine.details ;5MC STANDS FOR 5-METHYLCYTIDINE. THE STRUCTURE IS FORMED OF FOUR EQUIVALENT 5MCCT STRANDS DESIGNATED A, B, C, D. STRANDS A AND C, CONNECTED BY TWO HEMI-PROTONATED BASE PAIRS (5MC1.5MC1+ AND C2.C2+), 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 5MC1.5MC1+ PAIRS WERE NOT INCORPORATED IN THE COMPUTATIONS. THOSE OF THE C2.C2+ PAIRS WERE ARBITRARILY LOCATED ON THE C2 RESIDUES OF STRANDS A AND B, RESPECTIVELY. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 106D _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 ? # _exptl.entry_id 106D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 106D _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 106D _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_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A MCY 1 "O3'" ? ? ? 1_555 A DC 2 P ? ? A MCY 1 A DC 2 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale2 covale both ? B MCY 1 "O3'" ? ? ? 1_555 B DC 2 P ? ? B MCY 4 B DC 5 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale3 covale both ? C MCY 1 "O3'" ? ? ? 1_555 C DC 2 P ? ? C MCY 7 C DC 8 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale4 covale both ? D MCY 1 "O3'" ? ? ? 1_555 D DC 2 P ? ? D MCY 10 D DC 11 1_555 ? ? ? ? ? ? ? 1.613 ? ? hydrog1 hydrog ? ? A MCY 1 N3 ? ? ? 1_555 C MCY 1 N4 ? ? A MCY 1 C MCY 7 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog2 hydrog ? ? A MCY 1 N4 ? ? ? 1_555 C MCY 1 N3 ? ? A MCY 1 C MCY 7 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog3 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DC 2 N3 ? ? A DC 2 B DC 5 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 C DC 2 O2 ? ? A DC 2 C DC 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 C DC 2 N4 ? ? A DC 2 C DC 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog6 hydrog ? ? B MCY 1 N4 ? ? ? 1_555 D MCY 1 O2 ? ? B MCY 4 D MCY 10 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog7 hydrog ? ? B MCY 1 O2 ? ? ? 1_555 D MCY 1 N4 ? ? B MCY 4 D MCY 10 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog8 hydrog ? ? B DC 2 N4 ? ? ? 1_555 D DC 2 O2 ? ? B DC 5 D DC 11 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog9 hydrog ? ? B DC 2 O2 ? ? ? 1_555 D DC 2 N4 ? ? B DC 5 D DC 11 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 106D _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 106D _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 # _atom_sites_footnote.id 1 _atom_sites_footnote.text ;SOME OF THE CYTIDINES ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES HAVE BEEN ASSIGNED THE RESIDUE NAME C IN THE ENTRY AND ATOM H3 HAS BEEN FOOTNOTED. ; # 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 MCY 1 1 1 MCY MCY A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DT 3 3 3 DT DT A . n B 1 1 MCY 1 4 4 MCY MCY B . n B 1 2 DC 2 5 5 DC DC B . n B 1 3 DT 3 6 6 DT DT B . n C 1 1 MCY 1 7 7 MCY MCY C . n C 1 2 DC 2 8 8 DC DC C . n C 1 3 DT 3 9 9 DT DT C . n D 1 1 MCY 1 10 10 MCY MCY D . n D 1 2 DC 2 11 11 DC DC D . n D 1 3 DT 3 12 12 DT DT D . 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 MCY 1 A MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 2 B MCY 1 B MCY 4 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 3 C MCY 1 C MCY 7 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 4 D MCY 1 D MCY 10 ? DC "5-METHYL-2'-DEOXYCYTIDINE" # _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 # 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 # _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 5 4 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_site' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # 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 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_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 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 2 "HO3'" B DT 6 ? ? "HO5'" C MCY 7 ? ? 1.26 2 8 "HO5'" B MCY 4 ? ? "HO3'" C DT 9 ? ? 1.24 3 8 "HO3'" B DT 6 ? ? "HO5'" C MCY 7 ? ? 1.34 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.21 108.30 2.91 0.30 N 2 1 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.15 119.90 3.25 0.50 N 3 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.79 108.30 2.49 0.30 N 4 1 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.31 108.30 2.01 0.30 N 5 1 C2 B DC 5 ? ? N3 B DC 5 ? ? C4 B DC 5 ? ? 123.14 119.90 3.24 0.50 N 6 1 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 110.98 108.30 2.68 0.30 N 7 1 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.47 108.30 2.17 0.30 N 8 1 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 111.03 108.30 2.73 0.30 N 9 1 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.04 108.30 2.74 0.30 N 10 1 "O4'" D DT 12 ? ? "C1'" D DT 12 ? ? N1 D DT 12 ? ? 111.17 108.30 2.87 0.30 N 11 2 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.58 108.30 2.28 0.30 N 12 2 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.08 119.90 3.18 0.50 N 13 2 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.74 108.30 2.44 0.30 N 14 2 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.12 108.30 1.82 0.30 N 15 2 C2 B DC 5 ? ? N3 B DC 5 ? ? C4 B DC 5 ? ? 123.27 119.90 3.37 0.50 N 16 2 N1 B DC 5 ? ? C2 B DC 5 ? ? O2 B DC 5 ? ? 122.73 118.90 3.83 0.60 N 17 2 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 111.03 108.30 2.73 0.30 N 18 2 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.58 108.30 2.28 0.30 N 19 2 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 110.81 108.30 2.51 0.30 N 20 2 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 110.93 108.30 2.63 0.30 N 21 2 "O4'" D DT 12 ? ? "C1'" D DT 12 ? ? N1 D DT 12 ? ? 110.83 108.30 2.53 0.30 N 22 3 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.57 108.30 2.27 0.30 N 23 3 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.12 119.90 3.22 0.50 N 24 3 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.81 108.30 2.51 0.30 N 25 3 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.53 108.30 2.23 0.30 N 26 3 C2 B DC 5 ? ? N3 B DC 5 ? ? C4 B DC 5 ? ? 123.19 119.90 3.29 0.50 N 27 3 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 110.91 108.30 2.61 0.30 N 28 3 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.66 108.30 2.36 0.30 N 29 3 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 110.69 108.30 2.39 0.30 N 30 3 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.29 108.30 2.99 0.30 N 31 3 "O4'" D DT 12 ? ? "C1'" D DT 12 ? ? N1 D DT 12 ? ? 110.85 108.30 2.55 0.30 N 32 4 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.30 108.30 3.00 0.30 N 33 4 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.08 119.90 3.18 0.50 N 34 4 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 111.06 108.30 2.76 0.30 N 35 4 C2 B DC 5 ? ? N3 B DC 5 ? ? C4 B DC 5 ? ? 123.09 119.90 3.19 0.50 N 36 4 N1 B DC 5 ? ? C2 B DC 5 ? ? O2 B DC 5 ? ? 122.62 118.90 3.72 0.60 N 37 4 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 111.11 108.30 2.81 0.30 N 38 4 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 111.36 108.30 3.06 0.30 N 39 4 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 111.03 108.30 2.73 0.30 N 40 4 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 110.83 108.30 2.53 0.30 N 41 4 "O4'" D DT 12 ? ? "C1'" D DT 12 ? ? N1 D DT 12 ? ? 111.03 108.30 2.73 0.30 N 42 5 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.76 108.30 2.46 0.30 N 43 5 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.21 119.90 3.31 0.50 N 44 5 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 111.02 108.30 2.72 0.30 N 45 5 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.81 108.30 2.51 0.30 N 46 5 C2 B DC 5 ? ? N3 B DC 5 ? ? C4 B DC 5 ? ? 123.24 119.90 3.34 0.50 N 47 5 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 111.18 108.30 2.88 0.30 N 48 5 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.56 108.30 2.26 0.30 N 49 5 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 110.70 108.30 2.40 0.30 N 50 5 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 110.76 108.30 2.46 0.30 N 51 5 "O4'" D DT 12 ? ? "C1'" D DT 12 ? ? N1 D DT 12 ? ? 110.85 108.30 2.55 0.30 N 52 6 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.46 108.30 2.16 0.30 N 53 6 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.17 119.90 3.27 0.50 N 54 6 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.97 108.30 2.67 0.30 N 55 6 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.35 108.30 2.05 0.30 N 56 6 C2 B DC 5 ? ? N3 B DC 5 ? ? C4 B DC 5 ? ? 123.21 119.90 3.31 0.50 N 57 6 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 111.00 108.30 2.70 0.30 N 58 6 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.72 108.30 2.42 0.30 N 59 6 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 110.81 108.30 2.51 0.30 N 60 6 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 110.63 108.30 2.33 0.30 N 61 6 "O4'" D DT 12 ? ? "C1'" D DT 12 ? ? N1 D DT 12 ? ? 110.90 108.30 2.60 0.30 N 62 7 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.70 108.30 2.40 0.30 N 63 7 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.19 119.90 3.29 0.50 N 64 7 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.81 108.30 2.51 0.30 N 65 7 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.69 108.30 2.39 0.30 N 66 7 C2 B DC 5 ? ? N3 B DC 5 ? ? C4 B DC 5 ? ? 123.14 119.90 3.24 0.50 N 67 7 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 110.88 108.30 2.58 0.30 N 68 7 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.88 108.30 2.58 0.30 N 69 7 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 110.74 108.30 2.44 0.30 N 70 7 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 110.39 108.30 2.09 0.30 N 71 7 "O4'" D DT 12 ? ? "C1'" D DT 12 ? ? N1 D DT 12 ? ? 110.97 108.30 2.67 0.30 N 72 8 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.45 108.30 2.15 0.30 N 73 8 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.23 119.90 3.33 0.50 N 74 8 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.91 108.30 2.61 0.30 N 75 8 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.48 108.30 2.18 0.30 N 76 8 C2 B DC 5 ? ? N3 B DC 5 ? ? C4 B DC 5 ? ? 123.22 119.90 3.32 0.50 N 77 8 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 110.78 108.30 2.48 0.30 N 78 8 "O4'" C DC 8 ? ? "C1'" C DC 8 ? ? N1 C DC 8 ? ? 110.70 108.30 2.40 0.30 N 79 8 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 111.38 108.30 3.08 0.30 N 80 8 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 110.58 108.30 2.28 0.30 N 81 8 "O4'" D DT 12 ? ? "C1'" D DT 12 ? ? N1 D DT 12 ? ? 110.88 108.30 2.58 0.30 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 106D 'double helix' 106D '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 MCY 1 1_555 C MCY 1 1_555 2.094 0.183 -0.173 -21.458 12.891 179.007 1 A_MCY1:MCY7_C A 1 ? C 7 ? 14 2 1 D DC 2 1_555 B DC 2 1_555 2.486 2.477 0.743 11.400 31.811 178.287 2 D_DC11:DC5_B D 11 ? B 5 ? 15 2 1 A DC 2 1_555 C DC 2 1_555 -2.238 -2.274 -0.070 -6.151 -26.612 -179.371 3 A_DC2:DC8_C A 2 ? C 8 ? 15 2 1 D MCY 1 1_555 B MCY 1 1_555 2.423 2.151 -0.074 -8.183 13.564 179.363 4 D_MCY10:MCY4_B D 10 ? B 4 ? 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 MCY 1 1_555 C MCY 1 1_555 D DC 2 1_555 B DC 2 1_555 -2.981 3.287 -0.211 127.617 112.622 -42.438 -1.596 -1.555 -0.021 -58.376 66.149 -170.870 1 AD_MCY1DC11:DC5MCY7_BC A 1 ? C 7 ? 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 -1.812 -0.708 0.932 96.575 -144.398 -47.266 0.814 -0.600 0.757 73.763 49.333 -174.244 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 MCY 1 1_555 B MCY 1 1_555 3.440 2.525 -0.022 106.663 -144.428 -43.065 -1.274 1.712 -0.019 72.330 53.417 -179.577 3 AD_DC2MCY10:MCY4DC8_BC A 2 ? C 8 ? D 10 ? B 4 ? #