data_1NTT # _entry.id 1NTT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 1NTT pdb_00001ntt 10.2210/pdb1ntt/pdb RCSB RCSB018196 ? ? WWPDB D_1000018196 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2003-06-10 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2021-07-28 5 'Structure model' 2 1 2024-05-01 # _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' 'Atomic model' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Non-polymer description' 7 4 'Structure model' 'Polymer sequence' 8 4 'Structure model' 'Structure summary' 9 5 'Structure model' 'Data collection' 10 5 'Structure model' 'Database references' # 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' atom_site 2 4 'Structure model' chem_comp 3 4 'Structure model' entity 4 4 'Structure model' entity_poly 5 4 'Structure model' pdbx_nmr_software 6 4 'Structure model' pdbx_struct_assembly 7 4 'Structure model' pdbx_struct_oper_list 8 4 'Structure model' struct_conn 9 5 'Structure model' chem_comp_atom 10 5 'Structure model' chem_comp_bond 11 5 'Structure model' database_2 # 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' '_atom_site.Cartn_x' 2 4 'Structure model' '_atom_site.Cartn_y' 3 4 'Structure model' '_atom_site.Cartn_z' 4 4 'Structure model' '_atom_site.auth_atom_id' 5 4 'Structure model' '_atom_site.label_atom_id' 6 4 'Structure model' '_chem_comp.formula' 7 4 'Structure model' '_chem_comp.formula_weight' 8 4 'Structure model' '_chem_comp.mon_nstd_flag' 9 4 'Structure model' '_entity.formula_weight' 10 4 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 11 4 'Structure model' '_pdbx_nmr_software.name' 12 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 13 5 'Structure model' '_database_2.pdbx_DOI' 14 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NTT _pdbx_database_status.recvd_initial_deposition_date 2003-01-30 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _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 1NTQ 'DNA:RNA hybrid with same sequence' unspecified PDB 1NTS 'DNA:RNA hybrid with propynylated bases 1-7 in DNA strand' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Znosko, B.M.' 1 'Barnes III, T.W.' 2 'Krugh, T.R.' 3 'Turner, D.H.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'NMR Studies of DNA Single Strands and DNA:RNA Hybrids With and Without 1-Propynylation at C5 of Oligopyrimidines' J.Am.Chem.Soc. 125 6090 6097 2003 JACSAT US 0002-7863 0004 ? 12785839 10.1021/ja021285d 1 'Long-Range Cooperativity in Molecular Recognition of RNA by Oligodeoxynucleotides with Multiple C5-(1-Propynyl) Pyrimidines' J.Am.Chem.Soc. 123 4107 4118 2001 JACSAT US 0002-7863 0004 ? ? 10.1021/ja003208t # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Znosko, B.M.' 1 ? primary 'Barnes III, T.W.' 2 ? primary 'Krugh, T.R.' 3 ? primary 'Turner, D.H.' 4 ? 1 'Barnes III, T.W.' 5 ? 1 'Turner, D.H.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*AP*AP*AP*GP*GP*AP*GP*GP*A)-3'" 2981.895 1 ? ? ? ? 2 polymer syn "5'-D(*CP*(5PC)P*(PDU)P*(5PC)P*(5PC)P*(PDU)P*(PDU))-3'" 2210.558 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no AAAGGAGGA AAAGGAGGA A ? 2 polydeoxyribonucleotide no yes '(DC)(5PC)(PDU)(5PC)(5PC)(PDU)(PDU)' CCXCCXX B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A n 1 2 A n 1 3 A n 1 4 G n 1 5 G n 1 6 A n 1 7 G n 1 8 G n 1 9 A n 2 1 DC n 2 2 5PC n 2 3 PDU n 2 4 5PC n 2 5 5PC n 2 6 PDU n 2 7 PDU 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 5PC 'DNA linking' n "5(1-PROPYNYL)-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C12 H16 N3 O7 P' 345.245 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 PDU 'DNA linking' . "5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE" ? 'C12 H15 N2 O8 P' 346.230 # 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 A 1 2 2 A A A . n A 1 2 A 2 3 3 A A A . n A 1 3 A 3 4 4 A A A . n A 1 4 G 4 5 5 G G A . n A 1 5 G 5 6 6 G G A . n A 1 6 A 6 7 7 A A A . n A 1 7 G 7 8 8 G G A . n A 1 8 G 8 9 9 G G A . n A 1 9 A 9 10 10 A A A . n B 2 1 DC 1 1 1 DC C B . n B 2 2 5PC 2 2 2 5PC 5PC B . n B 2 3 PDU 3 3 3 PDU PDU B . n B 2 4 5PC 4 4 4 5PC 5PC B . n B 2 5 5PC 5 5 5 5PC 5PC B . n B 2 6 PDU 6 6 6 PDU PDU B . n B 2 7 PDU 7 7 7 PDU PDU B . n # _exptl.entry_id 1NTT _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _database_PDB_matrix.entry_id 1NTT _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 1NTT _struct.title ;5'(dCPCPUPCPCPUPUP)3':(rAGGAGGAAA)5', where P=propynyl ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1NTT _struct_keywords.pdbx_keywords RNA/DNA _struct_keywords.text 'DNA, RNA, hybrid, propynyl, RNA-DNA COMPLEX' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1NTT 1NTT ? ? ? 2 2 PDB 1NTT 1NTT ? ? ? # 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 1NTT A 1 ? 9 ? 1NTT 2 ? 10 ? 2 10 2 2 1NTT B 1 ? 7 ? 1NTT 1 ? 7 ? 1 7 # _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 ? _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_ _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 ? B DC 1 "O3'" ? ? ? 1_555 B 5PC 2 P ? ? B DC 1 B 5PC 2 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale2 covale both ? B 5PC 2 "O3'" ? ? ? 1_555 B PDU 3 P ? ? B 5PC 2 B PDU 3 1_555 ? ? ? ? ? ? ? 1.636 ? ? covale3 covale one ? B PDU 3 "O3'" ? ? ? 1_555 B 5PC 4 P ? ? B PDU 3 B 5PC 4 1_555 ? ? ? ? ? ? ? 1.631 ? ? covale4 covale both ? B 5PC 4 "O3'" ? ? ? 1_555 B 5PC 5 P ? ? B 5PC 4 B 5PC 5 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale5 covale both ? B 5PC 5 "O3'" ? ? ? 1_555 B PDU 6 P ? ? B 5PC 5 B PDU 6 1_555 ? ? ? ? ? ? ? 1.627 ? ? covale6 covale one ? B PDU 6 "O3'" ? ? ? 1_555 B PDU 7 P ? ? B PDU 6 B PDU 7 1_555 ? ? ? ? ? ? ? 1.625 ? ? hydrog1 hydrog ? ? A A 2 N1 ? ? ? 1_555 B PDU 7 N3 ? ? A A 3 B PDU 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 2 N6 ? ? ? 1_555 B PDU 7 O4 ? ? A A 3 B PDU 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A A 3 N1 ? ? ? 1_555 B PDU 6 N3 ? ? A A 4 B PDU 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 3 N6 ? ? ? 1_555 B PDU 6 O4 ? ? A A 4 B PDU 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 4 N1 ? ? ? 1_555 B 5PC 5 N3 ? ? A G 5 B 5PC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 4 N2 ? ? ? 1_555 B 5PC 5 O2 ? ? A G 5 B 5PC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 O6 ? ? ? 1_555 B 5PC 5 N4 ? ? A G 5 B 5PC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 5 N1 ? ? ? 1_555 B 5PC 4 N3 ? ? A G 6 B 5PC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 N2 ? ? ? 1_555 B 5PC 4 O2 ? ? A G 6 B 5PC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 O6 ? ? ? 1_555 B 5PC 4 N4 ? ? A G 6 B 5PC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 6 N1 ? ? ? 1_555 B PDU 3 N3 ? ? A A 7 B PDU 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 6 N6 ? ? ? 1_555 B PDU 3 O4 ? ? A A 7 B PDU 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 7 N1 ? ? ? 1_555 B 5PC 2 N3 ? ? A G 8 B 5PC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 N2 ? ? ? 1_555 B 5PC 2 O2 ? ? A G 8 B 5PC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 O6 ? ? ? 1_555 B 5PC 2 N4 ? ? A G 8 B 5PC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 B DC 1 N3 ? ? A G 9 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 N2 ? ? ? 1_555 B DC 1 O2 ? ? A G 9 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 8 O6 ? ? ? 1_555 B DC 1 N4 ? ? A G 9 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 N3 A A 2 ? ? C4 A A 2 ? ? 1.466 1.344 0.122 0.006 N 2 1 C4 A A 2 ? ? C5 A A 2 ? ? 1.460 1.383 0.077 0.007 N 3 1 N7 A A 2 ? ? C8 A A 2 ? ? 1.378 1.311 0.067 0.007 N 4 1 N3 A A 3 ? ? C4 A A 3 ? ? 1.465 1.344 0.121 0.006 N 5 1 C4 A A 3 ? ? C5 A A 3 ? ? 1.459 1.383 0.076 0.007 N 6 1 N7 A A 3 ? ? C8 A A 3 ? ? 1.378 1.311 0.067 0.007 N 7 1 N3 A A 4 ? ? C4 A A 4 ? ? 1.466 1.344 0.122 0.006 N 8 1 C4 A A 4 ? ? C5 A A 4 ? ? 1.459 1.383 0.076 0.007 N 9 1 N7 A A 4 ? ? C8 A A 4 ? ? 1.380 1.311 0.069 0.007 N 10 1 N1 A G 5 ? ? C2 A G 5 ? ? 1.467 1.373 0.094 0.008 N 11 1 N3 A G 5 ? ? C4 A G 5 ? ? 1.445 1.350 0.095 0.007 N 12 1 C4 A G 5 ? ? C5 A G 5 ? ? 1.437 1.379 0.058 0.007 N 13 1 C5 A G 5 ? ? C6 A G 5 ? ? 1.551 1.419 0.132 0.010 N 14 1 N7 A G 5 ? ? C8 A G 5 ? ? 1.377 1.305 0.072 0.006 N 15 1 N1 A G 6 ? ? C2 A G 6 ? ? 1.466 1.373 0.093 0.008 N 16 1 N3 A G 6 ? ? C4 A G 6 ? ? 1.448 1.350 0.098 0.007 N 17 1 C4 A G 6 ? ? C5 A G 6 ? ? 1.435 1.379 0.056 0.007 N 18 1 C5 A G 6 ? ? C6 A G 6 ? ? 1.549 1.419 0.130 0.010 N 19 1 N7 A G 6 ? ? C8 A G 6 ? ? 1.375 1.305 0.070 0.006 N 20 1 N3 A A 7 ? ? C4 A A 7 ? ? 1.466 1.344 0.122 0.006 N 21 1 C4 A A 7 ? ? C5 A A 7 ? ? 1.459 1.383 0.076 0.007 N 22 1 N7 A A 7 ? ? C8 A A 7 ? ? 1.378 1.311 0.067 0.007 N 23 1 N1 A G 8 ? ? C2 A G 8 ? ? 1.467 1.373 0.094 0.008 N 24 1 N3 A G 8 ? ? C4 A G 8 ? ? 1.444 1.350 0.094 0.007 N 25 1 C4 A G 8 ? ? C5 A G 8 ? ? 1.437 1.379 0.058 0.007 N 26 1 C5 A G 8 ? ? C6 A G 8 ? ? 1.552 1.419 0.133 0.010 N 27 1 N7 A G 8 ? ? C8 A G 8 ? ? 1.378 1.305 0.073 0.006 N 28 1 N1 A G 9 ? ? C2 A G 9 ? ? 1.466 1.373 0.093 0.008 N 29 1 N3 A G 9 ? ? C4 A G 9 ? ? 1.446 1.350 0.096 0.007 N 30 1 C4 A G 9 ? ? C5 A G 9 ? ? 1.437 1.379 0.058 0.007 N 31 1 C5 A G 9 ? ? C6 A G 9 ? ? 1.550 1.419 0.131 0.010 N 32 1 N7 A G 9 ? ? C8 A G 9 ? ? 1.377 1.305 0.072 0.006 N 33 1 N3 A A 10 ? ? C4 A A 10 ? ? 1.466 1.344 0.122 0.006 N 34 1 C4 A A 10 ? ? C5 A A 10 ? ? 1.458 1.383 0.075 0.007 N 35 1 N7 A A 10 ? ? C8 A A 10 ? ? 1.378 1.311 0.067 0.007 N 36 1 C4 B DC 1 ? ? N4 B DC 1 ? ? 1.407 1.335 0.072 0.009 N 37 1 N1 B DC 1 ? ? C6 B DC 1 ? ? 1.498 1.367 0.131 0.006 N 38 1 C2 B DC 1 ? ? N3 B DC 1 ? ? 1.470 1.353 0.117 0.008 N 39 1 C4 B DC 1 ? ? C5 B DC 1 ? ? 1.369 1.425 -0.056 0.008 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 C2 A A 2 ? ? N3 A A 2 ? ? C4 A A 2 ? ? 115.80 110.60 5.20 0.50 N 2 1 N3 A A 2 ? ? C4 A A 2 ? ? C5 A A 2 ? ? 117.39 126.80 -9.41 0.70 N 3 1 C5 A A 2 ? ? N7 A A 2 ? ? C8 A A 2 ? ? 97.46 103.90 -6.44 0.50 N 4 1 N7 A A 2 ? ? C8 A A 2 ? ? N9 A A 2 ? ? 122.40 113.80 8.60 0.50 N 5 1 C8 A A 2 ? ? N9 A A 2 ? ? C4 A A 2 ? ? 99.42 105.80 -6.38 0.40 N 6 1 N3 A A 2 ? ? C4 A A 2 ? ? N9 A A 2 ? ? 134.43 127.40 7.03 0.80 N 7 1 OP1 A A 3 ? ? P A A 3 ? ? OP2 A A 3 ? ? 109.53 119.60 -10.07 1.50 N 8 1 C2 A A 3 ? ? N3 A A 3 ? ? C4 A A 3 ? ? 115.66 110.60 5.06 0.50 N 9 1 N3 A A 3 ? ? C4 A A 3 ? ? C5 A A 3 ? ? 117.64 126.80 -9.16 0.70 N 10 1 C5 A A 3 ? ? N7 A A 3 ? ? C8 A A 3 ? ? 97.33 103.90 -6.57 0.50 N 11 1 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 122.22 113.80 8.42 0.50 N 12 1 C8 A A 3 ? ? N9 A A 3 ? ? C4 A A 3 ? ? 99.71 105.80 -6.09 0.40 N 13 1 N3 A A 3 ? ? C4 A A 3 ? ? N9 A A 3 ? ? 134.26 127.40 6.86 0.80 N 14 1 OP1 A A 4 ? ? P A A 4 ? ? OP2 A A 4 ? ? 109.55 119.60 -10.05 1.50 N 15 1 C2 A A 4 ? ? N3 A A 4 ? ? C4 A A 4 ? ? 115.71 110.60 5.11 0.50 N 16 1 N3 A A 4 ? ? C4 A A 4 ? ? C5 A A 4 ? ? 117.60 126.80 -9.20 0.70 N 17 1 C5 A A 4 ? ? N7 A A 4 ? ? C8 A A 4 ? ? 97.54 103.90 -6.36 0.50 N 18 1 N7 A A 4 ? ? C8 A A 4 ? ? N9 A A 4 ? ? 122.05 113.80 8.25 0.50 N 19 1 C8 A A 4 ? ? N9 A A 4 ? ? C4 A A 4 ? ? 99.77 105.80 -6.03 0.40 N 20 1 N3 A A 4 ? ? C4 A A 4 ? ? N9 A A 4 ? ? 134.23 127.40 6.83 0.80 N 21 1 OP1 A G 5 ? ? P A G 5 ? ? OP2 A G 5 ? ? 109.56 119.60 -10.04 1.50 N 22 1 C2 A G 5 ? ? N3 A G 5 ? ? C4 A G 5 ? ? 123.12 111.90 11.22 0.50 N 23 1 N3 A G 5 ? ? C4 A G 5 ? ? C5 A G 5 ? ? 117.75 128.60 -10.85 0.50 N 24 1 C5 A G 5 ? ? C6 A G 5 ? ? N1 A G 5 ? ? 115.16 111.50 3.66 0.50 N 25 1 C4 A G 5 ? ? C5 A G 5 ? ? N7 A G 5 ? ? 113.33 110.80 2.53 0.40 N 26 1 C5 A G 5 ? ? N7 A G 5 ? ? C8 A G 5 ? ? 97.00 104.30 -7.30 0.50 N 27 1 N7 A G 5 ? ? C8 A G 5 ? ? N9 A G 5 ? ? 121.90 113.10 8.80 0.50 N 28 1 C8 A G 5 ? ? N9 A G 5 ? ? C4 A G 5 ? ? 99.62 106.40 -6.78 0.40 N 29 1 N9 A G 5 ? ? C4 A G 5 ? ? C5 A G 5 ? ? 108.08 105.40 2.68 0.40 N 30 1 N3 A G 5 ? ? C4 A G 5 ? ? N9 A G 5 ? ? 134.15 126.00 8.15 0.60 N 31 1 C5 A G 5 ? ? C6 A G 5 ? ? O6 A G 5 ? ? 123.79 128.60 -4.81 0.60 N 32 1 OP1 A G 6 ? ? P A G 6 ? ? OP2 A G 6 ? ? 109.56 119.60 -10.04 1.50 N 33 1 C2 A G 6 ? ? N3 A G 6 ? ? C4 A G 6 ? ? 123.12 111.90 11.22 0.50 N 34 1 N3 A G 6 ? ? C4 A G 6 ? ? C5 A G 6 ? ? 117.69 128.60 -10.91 0.50 N 35 1 C5 A G 6 ? ? C6 A G 6 ? ? N1 A G 6 ? ? 115.32 111.50 3.82 0.50 N 36 1 C4 A G 6 ? ? C5 A G 6 ? ? N7 A G 6 ? ? 113.51 110.80 2.71 0.40 N 37 1 C5 A G 6 ? ? N7 A G 6 ? ? C8 A G 6 ? ? 97.06 104.30 -7.24 0.50 N 38 1 N7 A G 6 ? ? C8 A G 6 ? ? N9 A G 6 ? ? 121.82 113.10 8.72 0.50 N 39 1 C8 A G 6 ? ? N9 A G 6 ? ? C4 A G 6 ? ? 99.55 106.40 -6.85 0.40 N 40 1 N9 A G 6 ? ? C4 A G 6 ? ? C5 A G 6 ? ? 108.03 105.40 2.63 0.40 N 41 1 N3 A G 6 ? ? C4 A G 6 ? ? N9 A G 6 ? ? 134.27 126.00 8.27 0.60 N 42 1 C6 A G 6 ? ? C5 A G 6 ? ? N7 A G 6 ? ? 126.79 130.40 -3.61 0.60 N 43 1 C5 A G 6 ? ? C6 A G 6 ? ? O6 A G 6 ? ? 123.38 128.60 -5.22 0.60 N 44 1 OP1 A A 7 ? ? P A A 7 ? ? OP2 A A 7 ? ? 109.54 119.60 -10.06 1.50 N 45 1 C2 A A 7 ? ? N3 A A 7 ? ? C4 A A 7 ? ? 115.74 110.60 5.14 0.50 N 46 1 N3 A A 7 ? ? C4 A A 7 ? ? C5 A A 7 ? ? 117.54 126.80 -9.26 0.70 N 47 1 C5 A A 7 ? ? N7 A A 7 ? ? C8 A A 7 ? ? 97.53 103.90 -6.37 0.50 N 48 1 N7 A A 7 ? ? C8 A A 7 ? ? N9 A A 7 ? ? 122.06 113.80 8.26 0.50 N 49 1 C8 A A 7 ? ? N9 A A 7 ? ? C4 A A 7 ? ? 99.75 105.80 -6.05 0.40 N 50 1 N3 A A 7 ? ? C4 A A 7 ? ? N9 A A 7 ? ? 134.37 127.40 6.97 0.80 N 51 1 OP1 A G 8 ? ? P A G 8 ? ? OP2 A G 8 ? ? 109.47 119.60 -10.13 1.50 N 52 1 C2 A G 8 ? ? N3 A G 8 ? ? C4 A G 8 ? ? 123.06 111.90 11.16 0.50 N 53 1 N3 A G 8 ? ? C4 A G 8 ? ? C5 A G 8 ? ? 117.88 128.60 -10.72 0.50 N 54 1 C5 A G 8 ? ? C6 A G 8 ? ? N1 A G 8 ? ? 115.14 111.50 3.64 0.50 N 55 1 C4 A G 8 ? ? C5 A G 8 ? ? N7 A G 8 ? ? 113.28 110.80 2.48 0.40 N 56 1 C5 A G 8 ? ? N7 A G 8 ? ? C8 A G 8 ? ? 97.18 104.30 -7.12 0.50 N 57 1 N7 A G 8 ? ? C8 A G 8 ? ? N9 A G 8 ? ? 121.76 113.10 8.66 0.50 N 58 1 C8 A G 8 ? ? N9 A G 8 ? ? C4 A G 8 ? ? 99.50 106.40 -6.90 0.40 N 59 1 N9 A G 8 ? ? C4 A G 8 ? ? C5 A G 8 ? ? 108.25 105.40 2.85 0.40 N 60 1 N3 A G 8 ? ? C4 A G 8 ? ? N9 A G 8 ? ? 133.84 126.00 7.84 0.60 N 61 1 C5 A G 8 ? ? C6 A G 8 ? ? O6 A G 8 ? ? 123.93 128.60 -4.67 0.60 N 62 1 OP1 A G 9 ? ? P A G 9 ? ? OP2 A G 9 ? ? 109.46 119.60 -10.14 1.50 N 63 1 C2 A G 9 ? ? N3 A G 9 ? ? C4 A G 9 ? ? 122.99 111.90 11.09 0.50 N 64 1 N3 A G 9 ? ? C4 A G 9 ? ? C5 A G 9 ? ? 117.88 128.60 -10.72 0.50 N 65 1 C5 A G 9 ? ? C6 A G 9 ? ? N1 A G 9 ? ? 115.15 111.50 3.65 0.50 N 66 1 C4 A G 9 ? ? C5 A G 9 ? ? N7 A G 9 ? ? 113.33 110.80 2.53 0.40 N 67 1 C5 A G 9 ? ? N7 A G 9 ? ? C8 A G 9 ? ? 96.92 104.30 -7.38 0.50 N 68 1 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 121.88 113.10 8.78 0.50 N 69 1 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 99.82 106.40 -6.58 0.40 N 70 1 N9 A G 9 ? ? C4 A G 9 ? ? C5 A G 9 ? ? 107.94 105.40 2.54 0.40 N 71 1 N3 A G 9 ? ? C4 A G 9 ? ? N9 A G 9 ? ? 134.16 126.00 8.16 0.60 N 72 1 C5 A G 9 ? ? C6 A G 9 ? ? O6 A G 9 ? ? 123.80 128.60 -4.80 0.60 N 73 1 OP1 A A 10 ? ? P A A 10 ? ? OP2 A A 10 ? ? 109.42 119.60 -10.18 1.50 N 74 1 C2 A A 10 ? ? N3 A A 10 ? ? C4 A A 10 ? ? 115.72 110.60 5.12 0.50 N 75 1 N3 A A 10 ? ? C4 A A 10 ? ? C5 A A 10 ? ? 117.53 126.80 -9.27 0.70 N 76 1 C5 A A 10 ? ? N7 A A 10 ? ? C8 A A 10 ? ? 97.55 103.90 -6.35 0.50 N 77 1 N7 A A 10 ? ? C8 A A 10 ? ? N9 A A 10 ? ? 122.06 113.80 8.26 0.50 N 78 1 C8 A A 10 ? ? N9 A A 10 ? ? C4 A A 10 ? ? 99.72 105.80 -6.08 0.40 N 79 1 N3 A A 10 ? ? C4 A A 10 ? ? N9 A A 10 ? ? 134.35 127.40 6.95 0.80 N 80 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 111.87 108.30 3.57 0.30 N 81 1 C6 B DC 1 ? ? N1 B DC 1 ? ? C2 B DC 1 ? ? 117.26 120.30 -3.04 0.40 N 82 1 C4 B DC 1 ? ? C5 B DC 1 ? ? C6 B DC 1 ? ? 121.03 117.40 3.63 0.50 N 83 1 "C3'" B 5PC 2 ? ? "O3'" B 5PC 2 ? ? P B PDU 3 ? ? 128.32 119.70 8.62 1.20 Y # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id A _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 2 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.063 _pdbx_validate_planes.type 'SIDE CHAIN' # 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 B 5PC 2 B 5PC 2 ? DC ? 2 B PDU 3 B PDU 3 ? DU ? 3 B 5PC 4 B 5PC 4 ? DC ? 4 B 5PC 5 B 5PC 5 ? DC ? 5 B PDU 6 B PDU 6 ? DU ? 6 B PDU 7 B PDU 7 ? DU ? # _pdbx_nmr_ensemble.entry_id 1NTT _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? # _pdbx_nmr_representative.entry_id 1NTT _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '~1mM hybrid, 80 mM NaCl, 10 mM phosphate buffer, 0.5 mM EDTA, 90% H2O, 10% D2O' '90% H2O/10% D2O' 2 '~2.5 mM hybrid, 80 mM NaCl, 10 mM phosphate, 0.5 mM EDTA, 99.996% D2O' '99.996% D2O' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 273 ambient 7.0 '80 mM NaCl' ? K 2 303 ambient 7.0 '80 mM NaCl' ? K # _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.solution_id 2 _pdbx_nmr_exptl.conditions_id 2 _pdbx_nmr_exptl.type '2D NOESY' # _pdbx_nmr_refine.entry_id 1NTT _pdbx_nmr_refine.method 'simulated annealing, energy minimization' _pdbx_nmr_refine.details ;The structure is based on a total of 160 interproton distance restraints, 18 hydrogen bond restraints, and 59 dihedral angle restraints. ; _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal VNMR 5.2 collection Varian 1 Felix 2000 'data analysis' MSI 2 Discover 95.0 'structure solution' MSI 3 Discover 95.0 refinement MSI 4 # 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 5PC OP3 O N N 1 5PC P P N N 2 5PC OP1 O N N 3 5PC OP2 O N N 4 5PC "C5'" C N N 5 5PC "O5'" O N N 6 5PC "C4'" C N R 7 5PC "O4'" O N N 8 5PC "C3'" C N S 9 5PC "O3'" O N N 10 5PC "C2'" C N N 11 5PC "C1'" C N R 12 5PC N1 N N N 13 5PC C2 C N N 14 5PC O2 O N N 15 5PC N3 N N N 16 5PC C4 C N N 17 5PC N4 N N N 18 5PC C5 C N N 19 5PC C6 C N N 20 5PC C7 C N N 21 5PC C8 C N N 22 5PC C9 C N N 23 5PC HOP3 H N N 24 5PC HOP2 H N N 25 5PC "H5'" H N N 26 5PC "H5''" H N N 27 5PC "H4'" H N N 28 5PC "H3'" H N N 29 5PC "HO3'" H N N 30 5PC "H2'" H N N 31 5PC "H2''" H N N 32 5PC "H1'" H N N 33 5PC H41 H N N 34 5PC H42 H N N 35 5PC H6 H N N 36 5PC H91 H N N 37 5PC H92 H N N 38 5PC H93 H N N 39 A OP3 O N N 40 A P P N N 41 A OP1 O N N 42 A OP2 O N N 43 A "O5'" O N N 44 A "C5'" C N N 45 A "C4'" C N R 46 A "O4'" O N N 47 A "C3'" C N S 48 A "O3'" O N N 49 A "C2'" C N R 50 A "O2'" O N N 51 A "C1'" C N R 52 A N9 N Y N 53 A C8 C Y N 54 A N7 N Y N 55 A C5 C Y N 56 A C6 C Y N 57 A N6 N N N 58 A N1 N Y N 59 A C2 C Y N 60 A N3 N Y N 61 A C4 C Y N 62 A HOP3 H N N 63 A HOP2 H N N 64 A "H5'" H N N 65 A "H5''" H N N 66 A "H4'" H N N 67 A "H3'" H N N 68 A "HO3'" H N N 69 A "H2'" H N N 70 A "HO2'" H N N 71 A "H1'" H N N 72 A H8 H N N 73 A H61 H N N 74 A H62 H N N 75 A H2 H N N 76 DC OP3 O N N 77 DC P P N N 78 DC OP1 O N N 79 DC OP2 O N N 80 DC "O5'" O N N 81 DC "C5'" C N N 82 DC "C4'" C N R 83 DC "O4'" O N N 84 DC "C3'" C N S 85 DC "O3'" O N N 86 DC "C2'" C N N 87 DC "C1'" C N R 88 DC N1 N N N 89 DC C2 C N N 90 DC O2 O N N 91 DC N3 N N N 92 DC C4 C N N 93 DC N4 N N N 94 DC C5 C N N 95 DC C6 C N N 96 DC HOP3 H N N 97 DC HOP2 H N N 98 DC "H5'" H N N 99 DC "H5''" H N N 100 DC "H4'" H N N 101 DC "H3'" H N N 102 DC "HO3'" H N N 103 DC "H2'" H N N 104 DC "H2''" H N N 105 DC "H1'" H N N 106 DC H41 H N N 107 DC H42 H N N 108 DC H5 H N N 109 DC H6 H N N 110 G OP3 O N N 111 G P P N N 112 G OP1 O N N 113 G OP2 O N N 114 G "O5'" O N N 115 G "C5'" C N N 116 G "C4'" C N R 117 G "O4'" O N N 118 G "C3'" C N S 119 G "O3'" O N N 120 G "C2'" C N R 121 G "O2'" O N N 122 G "C1'" C N R 123 G N9 N Y N 124 G C8 C Y N 125 G N7 N Y N 126 G C5 C Y N 127 G C6 C N N 128 G O6 O N N 129 G N1 N N N 130 G C2 C N N 131 G N2 N N N 132 G N3 N N N 133 G C4 C Y N 134 G HOP3 H N N 135 G HOP2 H N N 136 G "H5'" H N N 137 G "H5''" H N N 138 G "H4'" H N N 139 G "H3'" H N N 140 G "HO3'" H N N 141 G "H2'" H N N 142 G "HO2'" H N N 143 G "H1'" H N N 144 G H8 H N N 145 G H1 H N N 146 G H21 H N N 147 G H22 H N N 148 PDU P P N N 149 PDU OP2 O N N 150 PDU OP1 O N N 151 PDU "O5'" O N N 152 PDU "C5'" C N N 153 PDU "C4'" C N R 154 PDU "O4'" O N N 155 PDU "C3'" C N S 156 PDU "O3'" O N N 157 PDU "C2'" C N N 158 PDU "C1'" C N R 159 PDU N1 N N N 160 PDU C2 C N N 161 PDU O2 O N N 162 PDU N3 N N N 163 PDU C4 C N N 164 PDU O4 O N N 165 PDU C5 C N N 166 PDU C5A C N N 167 PDU C5B C N N 168 PDU C5M C N N 169 PDU C6 C N N 170 PDU OP3 O N N 171 PDU HOP2 H N N 172 PDU "H5'" H N N 173 PDU "H5''" H N N 174 PDU "H4'" H N N 175 PDU "H3'" H N N 176 PDU H2 H N N 177 PDU "H2''" H N N 178 PDU "H2'" H N N 179 PDU "H1'" H N N 180 PDU H3 H N N 181 PDU H71 H N N 182 PDU H72 H N N 183 PDU H73 H N N 184 PDU H6 H N N 185 PDU HOP3 H N N 186 # 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 5PC OP3 P sing N N 1 5PC OP3 HOP3 sing N N 2 5PC P OP1 doub N N 3 5PC P OP2 sing N N 4 5PC P "O5'" sing N N 5 5PC OP2 HOP2 sing N N 6 5PC "C5'" "O5'" sing N N 7 5PC "C5'" "C4'" sing N N 8 5PC "C5'" "H5'" sing N N 9 5PC "C5'" "H5''" sing N N 10 5PC "C4'" "O4'" sing N N 11 5PC "C4'" "C3'" sing N N 12 5PC "C4'" "H4'" sing N N 13 5PC "O4'" "C1'" sing N N 14 5PC "C3'" "O3'" sing N N 15 5PC "C3'" "C2'" sing N N 16 5PC "C3'" "H3'" sing N N 17 5PC "O3'" "HO3'" sing N N 18 5PC "C2'" "C1'" sing N N 19 5PC "C2'" "H2'" sing N N 20 5PC "C2'" "H2''" sing N N 21 5PC "C1'" N1 sing N N 22 5PC "C1'" "H1'" sing N N 23 5PC N1 C2 sing N N 24 5PC N1 C6 sing N N 25 5PC C2 O2 doub N N 26 5PC C2 N3 sing N N 27 5PC N3 C4 doub N N 28 5PC C4 N4 sing N N 29 5PC C4 C5 sing N N 30 5PC N4 H41 sing N N 31 5PC N4 H42 sing N N 32 5PC C5 C6 doub N N 33 5PC C5 C7 sing N N 34 5PC C6 H6 sing N N 35 5PC C7 C8 trip N N 36 5PC C8 C9 sing N N 37 5PC C9 H91 sing N N 38 5PC C9 H92 sing N N 39 5PC C9 H93 sing N N 40 A OP3 P sing N N 41 A OP3 HOP3 sing N N 42 A P OP1 doub N N 43 A P OP2 sing N N 44 A P "O5'" sing N N 45 A OP2 HOP2 sing N N 46 A "O5'" "C5'" sing N N 47 A "C5'" "C4'" sing N N 48 A "C5'" "H5'" sing N N 49 A "C5'" "H5''" sing N N 50 A "C4'" "O4'" sing N N 51 A "C4'" "C3'" sing N N 52 A "C4'" "H4'" sing N N 53 A "O4'" "C1'" sing N N 54 A "C3'" "O3'" sing N N 55 A "C3'" "C2'" sing N N 56 A "C3'" "H3'" sing N N 57 A "O3'" "HO3'" sing N N 58 A "C2'" "O2'" sing N N 59 A "C2'" "C1'" sing N N 60 A "C2'" "H2'" sing N N 61 A "O2'" "HO2'" sing N N 62 A "C1'" N9 sing N N 63 A "C1'" "H1'" sing N N 64 A N9 C8 sing Y N 65 A N9 C4 sing Y N 66 A C8 N7 doub Y N 67 A C8 H8 sing N N 68 A N7 C5 sing Y N 69 A C5 C6 sing Y N 70 A C5 C4 doub Y N 71 A C6 N6 sing N N 72 A C6 N1 doub Y N 73 A N6 H61 sing N N 74 A N6 H62 sing N N 75 A N1 C2 sing Y N 76 A C2 N3 doub Y N 77 A C2 H2 sing N N 78 A N3 C4 sing Y N 79 DC OP3 P sing N N 80 DC OP3 HOP3 sing N N 81 DC P OP1 doub N N 82 DC P OP2 sing N N 83 DC P "O5'" sing N N 84 DC OP2 HOP2 sing N N 85 DC "O5'" "C5'" sing N N 86 DC "C5'" "C4'" sing N N 87 DC "C5'" "H5'" sing N N 88 DC "C5'" "H5''" sing N N 89 DC "C4'" "O4'" sing N N 90 DC "C4'" "C3'" sing N N 91 DC "C4'" "H4'" sing N N 92 DC "O4'" "C1'" sing N N 93 DC "C3'" "O3'" sing N N 94 DC "C3'" "C2'" sing N N 95 DC "C3'" "H3'" sing N N 96 DC "O3'" "HO3'" sing N N 97 DC "C2'" "C1'" sing N N 98 DC "C2'" "H2'" sing N N 99 DC "C2'" "H2''" sing N N 100 DC "C1'" N1 sing N N 101 DC "C1'" "H1'" sing N N 102 DC N1 C2 sing N N 103 DC N1 C6 sing N N 104 DC C2 O2 doub N N 105 DC C2 N3 sing N N 106 DC N3 C4 doub N N 107 DC C4 N4 sing N N 108 DC C4 C5 sing N N 109 DC N4 H41 sing N N 110 DC N4 H42 sing N N 111 DC C5 C6 doub N N 112 DC C5 H5 sing N N 113 DC C6 H6 sing N N 114 G OP3 P sing N N 115 G OP3 HOP3 sing N N 116 G P OP1 doub N N 117 G P OP2 sing N N 118 G P "O5'" sing N N 119 G OP2 HOP2 sing N N 120 G "O5'" "C5'" sing N N 121 G "C5'" "C4'" sing N N 122 G "C5'" "H5'" sing N N 123 G "C5'" "H5''" sing N N 124 G "C4'" "O4'" sing N N 125 G "C4'" "C3'" sing N N 126 G "C4'" "H4'" sing N N 127 G "O4'" "C1'" sing N N 128 G "C3'" "O3'" sing N N 129 G "C3'" "C2'" sing N N 130 G "C3'" "H3'" sing N N 131 G "O3'" "HO3'" sing N N 132 G "C2'" "O2'" sing N N 133 G "C2'" "C1'" sing N N 134 G "C2'" "H2'" sing N N 135 G "O2'" "HO2'" sing N N 136 G "C1'" N9 sing N N 137 G "C1'" "H1'" sing N N 138 G N9 C8 sing Y N 139 G N9 C4 sing Y N 140 G C8 N7 doub Y N 141 G C8 H8 sing N N 142 G N7 C5 sing Y N 143 G C5 C6 sing N N 144 G C5 C4 doub Y N 145 G C6 O6 doub N N 146 G C6 N1 sing N N 147 G N1 C2 sing N N 148 G N1 H1 sing N N 149 G C2 N2 sing N N 150 G C2 N3 doub N N 151 G N2 H21 sing N N 152 G N2 H22 sing N N 153 G N3 C4 sing N N 154 PDU C5M C5B sing N N 155 PDU OP1 P doub N N 156 PDU C5B C5A trip N N 157 PDU C5A C5 sing N N 158 PDU "C2'" "C3'" sing N N 159 PDU "C2'" "C1'" sing N N 160 PDU "C3'" "O3'" sing N N 161 PDU "C3'" "C4'" sing N N 162 PDU C5 C6 doub N N 163 PDU C5 C4 sing N N 164 PDU P "O5'" sing N N 165 PDU P OP2 sing N N 166 PDU "O5'" "C5'" sing N N 167 PDU O4 C4 doub N N 168 PDU C6 N1 sing N N 169 PDU C4 N3 sing N N 170 PDU "C5'" "C4'" sing N N 171 PDU N1 "C1'" sing N N 172 PDU N1 C2 sing N N 173 PDU "C4'" "O4'" sing N N 174 PDU N3 C2 sing N N 175 PDU "C1'" "O4'" sing N N 176 PDU C2 O2 doub N N 177 PDU P OP3 sing N N 178 PDU OP2 HOP2 sing N N 179 PDU "C5'" "H5'" sing N N 180 PDU "C5'" "H5''" sing N N 181 PDU "C4'" "H4'" sing N N 182 PDU "C3'" "H3'" sing N N 183 PDU "O3'" H2 sing N N 184 PDU "C2'" "H2''" sing N N 185 PDU "C2'" "H2'" sing N N 186 PDU "C1'" "H1'" sing N N 187 PDU N3 H3 sing N N 188 PDU C5M H71 sing N N 189 PDU C5M H72 sing N N 190 PDU C5M H73 sing N N 191 PDU C6 H6 sing N N 192 PDU OP3 HOP3 sing N N 193 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1NTT 'double helix' 1NTT 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A A 2 1_555 B PDU 7 1_555 -0.090 0.279 -0.242 -9.980 -13.535 1.980 1 A_A3:PDU7_B A 3 ? B 7 ? 20 1 1 A A 3 1_555 B PDU 6 1_555 -0.297 0.261 0.524 0.482 -16.681 3.526 2 A_A4:PDU6_B A 4 ? B 6 ? 20 1 1 A G 4 1_555 B 5PC 5 1_555 -1.383 -0.061 0.352 4.032 -17.768 1.148 3 A_G5:5PC5_B A 5 ? B 5 ? 19 1 1 A G 5 1_555 B 5PC 4 1_555 -0.479 0.132 -0.305 -2.769 -14.332 -6.331 4 A_G6:5PC4_B A 6 ? B 4 ? 19 1 1 A A 6 1_555 B PDU 3 1_555 -0.594 0.222 0.094 3.255 -14.110 -0.149 5 A_A7:PDU3_B A 7 ? B 3 ? 20 1 1 A G 7 1_555 B 5PC 2 1_555 -1.355 -0.032 0.252 5.741 -16.352 3.110 6 A_G8:5PC2_B A 8 ? B 2 ? 19 1 1 A G 8 1_555 B DC 1 1_555 -0.675 0.057 -0.460 -4.324 -22.792 -0.610 7 A_G9:DC1_B A 9 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A A 2 1_555 B PDU 7 1_555 A A 3 1_555 B PDU 6 1_555 0.428 -0.948 3.130 -4.077 1.942 29.871 -2.189 -1.599 2.980 3.740 7.853 30.203 1 AA_A3A4:PDU6PDU7_BB A 3 ? B 7 ? A 4 ? B 6 ? 1 A A 3 1_555 B PDU 6 1_555 A G 4 1_555 B 5PC 5 1_555 -0.128 -1.084 3.293 2.786 0.668 29.190 -2.285 0.853 3.242 1.322 -5.511 29.327 2 AA_A4G5:5PC5PDU6_BB A 4 ? B 6 ? A 5 ? B 5 ? 1 A G 4 1_555 B 5PC 5 1_555 A G 5 1_555 B 5PC 4 1_555 -0.580 -0.960 3.658 3.778 3.113 36.124 -2.008 1.502 3.489 4.991 -6.058 36.443 3 AA_G5G6:5PC45PC5_BB A 5 ? B 5 ? A 6 ? B 4 ? 1 A G 5 1_555 B 5PC 4 1_555 A A 6 1_555 B PDU 3 1_555 0.695 -0.947 3.279 -1.779 2.516 32.437 -2.120 -1.544 3.157 4.491 3.176 32.579 4 AA_G6A7:PDU35PC4_BB A 6 ? B 4 ? A 7 ? B 3 ? 1 A A 6 1_555 B PDU 3 1_555 A G 7 1_555 B 5PC 2 1_555 0.278 -1.415 3.306 -2.091 3.509 28.230 -3.657 -1.032 3.083 7.146 4.259 28.518 5 AA_A7G8:5PC2PDU3_BB A 7 ? B 3 ? A 8 ? B 2 ? 1 A G 7 1_555 B 5PC 2 1_555 A G 8 1_555 B DC 1 1_555 -0.496 -0.964 3.698 1.221 7.959 39.353 -2.403 0.876 3.430 11.671 -1.790 40.137 6 AA_G8G9:DC15PC2_BB A 8 ? B 2 ? A 9 ? B 1 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.field_strength 500 # _atom_sites.entry_id 1NTT _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_