data_1TOB # _entry.id 1TOB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1TOB WWPDB D_1000176766 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1TOB _pdbx_database_status.recvd_initial_deposition_date 1996-12-12 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _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 'Jiang, L.' 1 'Suri, A.K.' 2 'Fiala, R.' 3 'Patel, D.J.' 4 # _citation.id primary _citation.title 'Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex.' _citation.journal_abbrev Chem.Biol. _citation.journal_volume 4 _citation.page_first 35 _citation.page_last ? _citation.year 1997 _citation.journal_id_ASTM CBOLE2 _citation.country UK _citation.journal_id_ISSN 1074-5521 _citation.journal_id_CSD 2050 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9070426 _citation.pdbx_database_id_DOI '10.1016/S1074-5521(97)90235-0' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jiang, L.' 1 ? primary 'Suri, A.K.' 2 ? primary 'Fiala, R.' 3 ? primary 'Patel, D.J.' 4 ? # _cell.entry_id 1TOB _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 1TOB _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # 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 ;RNA (5'-R(GGCACGAGGUUUAGCUACACUCGUGCC)-3') ; 8641.168 1 ? ? ? ? 2 non-polymer man 3-ammonio-3-deoxy-alpha-D-glucopyranose 180.179 1 ? ? ? ? 3 non-polymer man 2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose 164.203 1 ? ? ? ? 4 non-polymer syn 1,3-DIAMINO-5,6-DIHYDROXYCYCLOHEXANE 148.203 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGCACGAGGUUUAGCUACACUCGUGCC _entity_poly.pdbx_seq_one_letter_code_can GGCACGAGGUUUAGCUACACUCGUGCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 A n 1 5 C n 1 6 G n 1 7 A n 1 8 G n 1 9 G n 1 10 U n 1 11 U n 1 12 U n 1 13 A n 1 14 G n 1 15 C n 1 16 U n 1 17 A n 1 18 C n 1 19 A n 1 20 C n 1 21 U n 1 22 C n 1 23 G n 1 24 U n 1 25 G n 1 26 C n 1 27 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 27 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 1TOB _struct_ref.pdbx_db_accession 1TOB _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1TOB _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 27 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1TOB _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 27 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 27 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 TOA 'D-saccharide, alpha linking' . 3-ammonio-3-deoxy-alpha-D-glucopyranose ? 'C6 H14 N O5 1' 180.179 TOB non-polymer . 1,3-DIAMINO-5,6-DIHYDROXYCYCLOHEXANE ? 'C6 H16 N2 O2 2' 148.203 TOC 'D-saccharide, alpha linking' . 2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose ? 'C6 H16 N2 O3 2' 164.203 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength 1 UNITYPLUS Varian 500 2 UNITYPLUS Varian 600 # _pdbx_nmr_refine.entry_id 1TOB _pdbx_nmr_refine.method 'RESTRAINED MOLECULAR DYNAMICS' _pdbx_nmr_refine.details 'RESTRAINED MOLECULAR DYNAMICS.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1TOB _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 7 _pdbx_nmr_ensemble.conformer_selection_criteria 'ENERGY (INCLUDING RESTRAINT ENERGY TERM)' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR 3.1 BRUNGER 1 'structure solution' X-PLOR 3.1 ? 2 # _exptl.entry_id 1TOB _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1TOB _struct.title 'SACCHARIDE-RNA RECOGNITION IN AN AMINOGLYCOSIDE ANTIBIOTIC-RNA APTAMER COMPLEX, NMR, 7 STRUCTURES' _struct.pdbx_descriptor 'AMINOGLYCOSIDE ANTIBIOTIC/RNA COMPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1TOB _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RIBONUCLEIC ACID, RNA' # 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 ? C N N 3 ? D N N 4 ? # 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 one ? B TOA . C1 ? ? ? 1_555 D TOB . O6 ? ? A TOA 28 A TOB 29 1_555 ? ? ? ? ? ? ? 1.382 ? ? covale2 covale none ? D TOB . C4 ? ? ? 1_555 C TOC . O1 ? ? A TOB 29 A TOC 30 1_555 ? ? ? ? ? ? ? 1.442 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 27 N3 ? ? A G 1 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 27 O2 ? ? A G 1 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 27 N4 ? ? A G 1 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 2 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 2 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 2 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 3 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 3 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 3 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 24 N3 ? ? A A 4 A U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 24 O4 ? ? A A 4 A U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 5 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 5 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 5 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 6 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 6 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 6 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 7 N1 ? ? ? 1_555 A U 21 N3 ? ? A A 7 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 7 N6 ? ? ? 1_555 A U 21 O4 ? ? A A 7 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 8 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 8 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 20 N4 ? ? A G 8 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 9 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 9 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 9 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 17 N1 ? ? A U 10 A A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 10 O4 ? ? ? 1_555 A A 17 N6 ? ? A U 10 A A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 11 N3 ? ? ? 1_555 A U 16 O4 ? ? A U 11 A U 16 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog29 hydrog ? ? A U 11 O2 ? ? ? 1_555 A U 16 N3 ? ? A U 11 A U 16 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1TOB _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 1TOB _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 A 4 4 4 A A A . n A 1 5 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n A 1 7 A 7 7 7 A A A . n A 1 8 G 8 8 8 G G A . n A 1 9 G 9 9 9 G G A . n A 1 10 U 10 10 10 U U A . n A 1 11 U 11 11 11 U U A . n A 1 12 U 12 12 12 U U A . n A 1 13 A 13 13 13 A A A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 U 16 16 16 U U A . n A 1 17 A 17 17 17 A A A . n A 1 18 C 18 18 18 C C A . n A 1 19 A 19 19 19 A A A . n A 1 20 C 20 20 20 C C A . n A 1 21 U 21 21 21 U U A . n A 1 22 C 22 22 22 C C A . n A 1 23 G 23 23 23 G G A . n A 1 24 U 24 24 24 U U A . n A 1 25 G 25 25 25 G G A . n A 1 26 C 26 26 26 C C A . n A 1 27 C 27 27 27 C C A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 TOA 1 28 28 TOA TOA A . C 3 TOC 1 30 30 TOC TOC A . D 4 TOB 1 29 29 TOB TOB A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,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 ? _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 1997-06-16 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2020-06-24 5 'Structure model' 2 0 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 5 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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 4 'Structure model' 'Source and taxonomy' 7 5 'Structure model' 'Atomic model' 8 5 'Structure model' 'Data collection' 9 5 'Structure model' 'Derived calculations' 10 5 'Structure model' 'Structure summary' # 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' ndb_struct_na_base_pair_step 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_entity_src_syn 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_ref 8 4 'Structure model' struct_ref_seq 9 5 'Structure model' atom_site 10 5 'Structure model' chem_comp 11 5 'Structure model' entity 12 5 'Structure model' pdbx_chem_comp_identifier 13 5 'Structure model' pdbx_entity_nonpoly 14 5 'Structure model' struct_site 15 5 'Structure model' struct_site_gen # 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' '_ndb_struct_na_base_pair_step.inclination' 2 4 'Structure model' '_pdbx_database_status.process_site' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 5 'Structure model' '_atom_site.auth_atom_id' 5 5 'Structure model' '_atom_site.label_atom_id' 6 5 'Structure model' '_chem_comp.name' 7 5 'Structure model' '_chem_comp.type' 8 5 'Structure model' '_entity.pdbx_description' 9 5 'Structure model' '_pdbx_entity_nonpoly.name' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 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 1 "HO2'" A G 6 ? ? OP1 A A 7 ? ? 1.51 2 2 O5 A TOA 28 ? ? HO5 A TOB 29 ? ? 1.56 3 4 O5 A TOA 28 ? ? HO5 A TOB 29 ? ? 1.48 # 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 3 N1 A C 15 ? ? C6 A C 15 ? ? 1.329 1.367 -0.038 0.006 N 2 4 N1 A C 15 ? ? C6 A C 15 ? ? 1.325 1.367 -0.042 0.006 N 3 4 "C2'" A G 23 ? ? "C1'" A G 23 ? ? 1.470 1.526 -0.056 0.008 N 4 5 N1 A C 15 ? ? C6 A C 15 ? ? 1.311 1.367 -0.056 0.006 N 5 6 N1 A C 15 ? ? C6 A C 15 ? ? 1.313 1.367 -0.054 0.006 N 6 7 N1 A C 15 ? ? C6 A C 15 ? ? 1.321 1.367 -0.046 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 112.80 108.50 4.30 0.70 N 2 1 "C1'" A G 2 ? ? "O4'" A G 2 ? ? "C4'" A G 2 ? ? 104.00 109.70 -5.70 0.70 N 3 1 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.74 108.50 4.24 0.70 N 4 1 "O4'" A A 4 ? ? "C1'" A A 4 ? ? N9 A A 4 ? ? 112.80 108.50 4.30 0.70 N 5 1 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 113.96 108.50 5.46 0.70 N 6 1 "O4'" A G 6 ? ? "C1'" A G 6 ? ? N9 A G 6 ? ? 115.59 108.50 7.09 0.70 N 7 1 "C3'" A G 6 ? ? "O3'" A G 6 ? ? P A A 7 ? ? 128.95 119.70 9.25 1.20 Y 8 1 "C1'" A A 7 ? ? "O4'" A A 7 ? ? "C4'" A A 7 ? ? 103.67 109.70 -6.03 0.70 N 9 1 "O4'" A A 7 ? ? "C1'" A A 7 ? ? "C2'" A A 7 ? ? 99.20 105.80 -6.60 1.00 N 10 1 "O4'" A U 11 ? ? "C1'" A U 11 ? ? N1 A U 11 ? ? 115.52 108.50 7.02 0.70 N 11 1 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 115.39 108.50 6.89 0.70 N 12 1 "O4'" A A 13 ? ? "C1'" A A 13 ? ? N9 A A 13 ? ? 113.19 108.50 4.69 0.70 N 13 1 "O4'" A G 14 ? ? "C1'" A G 14 ? ? N9 A G 14 ? ? 113.21 108.50 4.71 0.70 N 14 1 "C3'" A G 14 ? ? "O3'" A G 14 ? ? P A C 15 ? ? 127.38 119.70 7.68 1.20 Y 15 1 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 113.89 108.50 5.39 0.70 N 16 1 "O4'" A A 17 ? ? "C1'" A A 17 ? ? N9 A A 17 ? ? 113.96 108.50 5.46 0.70 N 17 1 "O4'" A C 18 ? ? "C1'" A C 18 ? ? N1 A C 18 ? ? 113.23 108.50 4.73 0.70 N 18 1 N1 A C 18 ? ? C2 A C 18 ? ? O2 A C 18 ? ? 122.62 118.90 3.72 0.60 N 19 1 "O4'" A C 20 ? ? "C1'" A C 20 ? ? N1 A C 20 ? ? 117.46 108.50 8.96 0.70 N 20 1 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 114.96 108.50 6.46 0.70 N 21 1 "C1'" A C 22 ? ? "O4'" A C 22 ? ? "C4'" A C 22 ? ? 104.29 109.70 -5.41 0.70 N 22 1 "O4'" A G 23 ? ? "C1'" A G 23 ? ? N9 A G 23 ? ? 113.53 108.50 5.03 0.70 N 23 1 "O4'" A U 24 ? ? "C1'" A U 24 ? ? N1 A U 24 ? ? 114.40 108.50 5.90 0.70 N 24 1 "O4'" A C 26 ? ? "C1'" A C 26 ? ? N1 A C 26 ? ? 114.43 108.50 5.93 0.70 N 25 2 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 112.76 108.50 4.26 0.70 N 26 2 "C1'" A G 2 ? ? "O4'" A G 2 ? ? "C4'" A G 2 ? ? 105.09 109.70 -4.61 0.70 N 27 2 "O4'" A A 4 ? ? "C1'" A A 4 ? ? N9 A A 4 ? ? 113.18 108.50 4.68 0.70 N 28 2 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 113.12 108.50 4.62 0.70 N 29 2 "O4'" A U 10 ? ? "C1'" A U 10 ? ? N1 A U 10 ? ? 112.70 108.50 4.20 0.70 N 30 2 "O4'" A U 11 ? ? "C1'" A U 11 ? ? N1 A U 11 ? ? 113.05 108.50 4.55 0.70 N 31 2 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 114.42 108.50 5.92 0.70 N 32 2 "C3'" A A 13 ? ? "O3'" A A 13 ? ? P A G 14 ? ? 129.80 119.70 10.10 1.20 Y 33 2 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 114.21 108.50 5.71 0.70 N 34 2 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.54 108.50 5.04 0.70 N 35 2 "O4'" A A 17 ? ? "C1'" A A 17 ? ? N9 A A 17 ? ? 113.17 108.50 4.67 0.70 N 36 2 "C1'" A C 18 ? ? "O4'" A C 18 ? ? "C4'" A C 18 ? ? 105.42 109.70 -4.28 0.70 N 37 2 "O4'" A C 18 ? ? "C1'" A C 18 ? ? N1 A C 18 ? ? 115.39 108.50 6.89 0.70 N 38 2 "O4'" A C 20 ? ? "C1'" A C 20 ? ? N1 A C 20 ? ? 114.89 108.50 6.39 0.70 N 39 2 "C3'" A U 21 ? ? "O3'" A U 21 ? ? P A C 22 ? ? 130.19 119.70 10.49 1.20 Y 40 2 "O4'" A G 23 ? ? "C1'" A G 23 ? ? N9 A G 23 ? ? 116.97 108.50 8.47 0.70 N 41 2 "O4'" A C 26 ? ? "C1'" A C 26 ? ? N1 A C 26 ? ? 113.99 108.50 5.49 0.70 N 42 3 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 114.53 108.50 6.03 0.70 N 43 3 "C1'" A G 2 ? ? "O4'" A G 2 ? ? "C4'" A G 2 ? ? 104.52 109.70 -5.18 0.70 N 44 3 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 112.97 108.50 4.47 0.70 N 45 3 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 113.28 108.50 4.78 0.70 N 46 3 "O4'" A G 6 ? ? "C1'" A G 6 ? ? N9 A G 6 ? ? 113.17 108.50 4.67 0.70 N 47 3 "C1'" A A 7 ? ? "O4'" A A 7 ? ? "C4'" A A 7 ? ? 105.17 109.70 -4.53 0.70 N 48 3 "O4'" A G 8 ? ? "C1'" A G 8 ? ? "C2'" A G 8 ? ? 99.53 105.80 -6.27 1.00 N 49 3 "O4'" A G 8 ? ? "C1'" A G 8 ? ? N9 A G 8 ? ? 115.32 108.50 6.82 0.70 N 50 3 "O4'" A G 9 ? ? "C1'" A G 9 ? ? N9 A G 9 ? ? 114.79 108.50 6.29 0.70 N 51 3 "C3'" A U 11 ? ? "O3'" A U 11 ? ? P A U 12 ? ? 127.48 119.70 7.78 1.20 Y 52 3 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 115.18 108.50 6.68 0.70 N 53 3 "C3'" A A 13 ? ? "O3'" A A 13 ? ? P A G 14 ? ? 128.56 119.70 8.86 1.20 Y 54 3 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 114.36 108.50 5.86 0.70 N 55 3 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 114.92 108.50 6.42 0.70 N 56 3 "O4'" A A 17 ? ? "C1'" A A 17 ? ? N9 A A 17 ? ? 112.96 108.50 4.46 0.70 N 57 3 "O4'" A C 18 ? ? "C1'" A C 18 ? ? N1 A C 18 ? ? 116.57 108.50 8.07 0.70 N 58 3 "O4'" A A 19 ? ? "C1'" A A 19 ? ? "C2'" A A 19 ? ? 98.48 105.80 -7.32 1.00 N 59 3 "C3'" A C 20 ? ? "O3'" A C 20 ? ? P A U 21 ? ? 129.43 119.70 9.73 1.20 Y 60 3 "O4'" A U 21 ? ? "C1'" A U 21 ? ? "C2'" A U 21 ? ? 97.70 105.80 -8.10 1.00 N 61 3 "C3'" A U 21 ? ? "O3'" A U 21 ? ? P A C 22 ? ? 127.19 119.70 7.49 1.20 Y 62 3 "C1'" A C 22 ? ? "O4'" A C 22 ? ? "C4'" A C 22 ? ? 103.90 109.70 -5.80 0.70 N 63 3 "O4'" A C 22 ? ? "C1'" A C 22 ? ? "C2'" A C 22 ? ? 98.57 105.80 -7.23 1.00 N 64 3 "C3'" A G 23 ? ? "C2'" A G 23 ? ? "C1'" A G 23 ? ? 106.83 101.50 5.33 0.80 N 65 3 "O4'" A G 23 ? ? "C1'" A G 23 ? ? N9 A G 23 ? ? 113.62 108.50 5.12 0.70 N 66 3 "O4'" A U 24 ? ? "C1'" A U 24 ? ? N1 A U 24 ? ? 113.96 108.50 5.46 0.70 N 67 3 "O4'" A C 26 ? ? "C1'" A C 26 ? ? N1 A C 26 ? ? 114.47 108.50 5.97 0.70 N 68 3 "O4'" A C 27 ? ? "C1'" A C 27 ? ? N1 A C 27 ? ? 114.01 108.50 5.51 0.70 N 69 4 "C1'" A G 2 ? ? "O4'" A G 2 ? ? "C4'" A G 2 ? ? 103.51 109.70 -6.19 0.70 N 70 4 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 113.40 108.50 4.90 0.70 N 71 4 "O4'" A A 7 ? ? "C1'" A A 7 ? ? N9 A A 7 ? ? 113.27 108.50 4.77 0.70 N 72 4 "C3'" A A 7 ? ? "O3'" A A 7 ? ? P A G 8 ? ? 127.20 119.70 7.50 1.20 Y 73 4 "O4'" A U 10 ? ? "C1'" A U 10 ? ? N1 A U 10 ? ? 115.43 108.50 6.93 0.70 N 74 4 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 114.73 108.50 6.23 0.70 N 75 4 "O4'" A A 13 ? ? "C1'" A A 13 ? ? N9 A A 13 ? ? 113.26 108.50 4.76 0.70 N 76 4 "C3'" A G 14 ? ? "O3'" A G 14 ? ? P A C 15 ? ? 128.10 119.70 8.40 1.20 Y 77 4 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 113.08 108.50 4.58 0.70 N 78 4 "O4'" A C 18 ? ? "C1'" A C 18 ? ? N1 A C 18 ? ? 113.17 108.50 4.67 0.70 N 79 4 N1 A C 18 ? ? C2 A C 18 ? ? O2 A C 18 ? ? 122.52 118.90 3.62 0.60 N 80 4 "O4'" A A 19 ? ? "C1'" A A 19 ? ? N9 A A 19 ? ? 113.40 108.50 4.90 0.70 N 81 4 "O4'" A C 20 ? ? "C1'" A C 20 ? ? "C2'" A C 20 ? ? 98.18 105.80 -7.62 1.00 N 82 4 "O4'" A C 20 ? ? "C1'" A C 20 ? ? N1 A C 20 ? ? 113.34 108.50 4.84 0.70 N 83 4 "C1'" A U 21 ? ? "O4'" A U 21 ? ? "C4'" A U 21 ? ? 101.62 109.70 -8.08 0.70 N 84 4 "O4'" A U 21 ? ? "C1'" A U 21 ? ? "C2'" A U 21 ? ? 99.42 105.80 -6.38 1.00 N 85 4 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 114.60 108.50 6.10 0.70 N 86 4 "C3'" A U 21 ? ? "O3'" A U 21 ? ? P A C 22 ? ? 127.51 119.70 7.81 1.20 Y 87 4 "C3'" A C 22 ? ? "O3'" A C 22 ? ? P A G 23 ? ? 130.53 119.70 10.83 1.20 Y 88 4 "O4'" A G 23 ? ? "C1'" A G 23 ? ? N9 A G 23 ? ? 113.75 108.50 5.25 0.70 N 89 4 "O4'" A U 24 ? ? "C1'" A U 24 ? ? N1 A U 24 ? ? 113.18 108.50 4.68 0.70 N 90 4 "O4'" A C 26 ? ? "C1'" A C 26 ? ? N1 A C 26 ? ? 114.16 108.50 5.66 0.70 N 91 5 "C1'" A G 1 ? ? "O4'" A G 1 ? ? "C4'" A G 1 ? ? 105.00 109.70 -4.70 0.70 N 92 5 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 116.57 108.50 8.07 0.70 N 93 5 "C1'" A G 2 ? ? "O4'" A G 2 ? ? "C4'" A G 2 ? ? 104.16 109.70 -5.54 0.70 N 94 5 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 113.38 108.50 4.88 0.70 N 95 5 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 115.16 108.50 6.66 0.70 N 96 5 "C3'" A A 13 ? ? "O3'" A A 13 ? ? P A G 14 ? ? 129.78 119.70 10.08 1.20 Y 97 5 "O4'" A G 14 ? ? "C1'" A G 14 ? ? N9 A G 14 ? ? 113.82 108.50 5.32 0.70 N 98 5 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 117.47 108.50 8.97 0.70 N 99 5 "C3'" A C 15 ? ? "O3'" A C 15 ? ? P A U 16 ? ? 127.85 119.70 8.15 1.20 Y 100 5 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.88 108.50 5.38 0.70 N 101 5 "O4'" A A 17 ? ? "C1'" A A 17 ? ? N9 A A 17 ? ? 116.15 108.50 7.65 0.70 N 102 5 "C3'" A C 18 ? ? "O3'" A C 18 ? ? P A A 19 ? ? 127.64 119.70 7.94 1.20 Y 103 5 "O4'" A C 20 ? ? "C1'" A C 20 ? ? "C2'" A C 20 ? ? 99.48 105.80 -6.32 1.00 N 104 5 N1 A C 20 ? ? C2 A C 20 ? ? O2 A C 20 ? ? 123.26 118.90 4.36 0.60 N 105 5 "C3'" A U 21 ? ? "O3'" A U 21 ? ? P A C 22 ? ? 129.51 119.70 9.81 1.20 Y 106 5 "C1'" A C 22 ? ? "O4'" A C 22 ? ? "C4'" A C 22 ? ? 103.52 109.70 -6.18 0.70 N 107 5 "O4'" A C 22 ? ? "C1'" A C 22 ? ? "C2'" A C 22 ? ? 97.92 105.80 -7.88 1.00 N 108 5 "C3'" A G 23 ? ? "C2'" A G 23 ? ? "C1'" A G 23 ? ? 106.56 101.50 5.06 0.80 N 109 5 "O4'" A G 23 ? ? "C1'" A G 23 ? ? N9 A G 23 ? ? 114.27 108.50 5.77 0.70 N 110 5 "O4'" A U 24 ? ? "C1'" A U 24 ? ? N1 A U 24 ? ? 113.62 108.50 5.12 0.70 N 111 5 "O4'" A C 26 ? ? "C1'" A C 26 ? ? N1 A C 26 ? ? 114.76 108.50 6.26 0.70 N 112 5 "O4'" A C 27 ? ? "C1'" A C 27 ? ? N1 A C 27 ? ? 113.73 108.50 5.23 0.70 N 113 6 "C1'" A G 2 ? ? "O4'" A G 2 ? ? "C4'" A G 2 ? ? 104.14 109.70 -5.56 0.70 N 114 6 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 112.79 108.50 4.29 0.70 N 115 6 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.85 108.50 4.35 0.70 N 116 6 "O4'" A A 4 ? ? "C1'" A A 4 ? ? N9 A A 4 ? ? 112.90 108.50 4.40 0.70 N 117 6 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 112.79 108.50 4.29 0.70 N 118 6 "O4'" A G 6 ? ? "C1'" A G 6 ? ? N9 A G 6 ? ? 113.11 108.50 4.61 0.70 N 119 6 "C3'" A G 6 ? ? "O3'" A G 6 ? ? P A A 7 ? ? 128.64 119.70 8.94 1.20 Y 120 6 "O4'" A A 7 ? ? "C1'" A A 7 ? ? "C2'" A A 7 ? ? 97.42 105.80 -8.38 1.00 N 121 6 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 114.95 108.50 6.45 0.70 N 122 6 "C3'" A A 13 ? ? "O3'" A A 13 ? ? P A G 14 ? ? 130.33 119.70 10.63 1.20 Y 123 6 "O4'" A G 14 ? ? "C1'" A G 14 ? ? N9 A G 14 ? ? 114.57 108.50 6.07 0.70 N 124 6 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 116.42 108.50 7.92 0.70 N 125 6 "C3'" A C 15 ? ? "O3'" A C 15 ? ? P A U 16 ? ? 128.56 119.70 8.86 1.20 Y 126 6 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.54 108.50 5.04 0.70 N 127 6 "O4'" A A 17 ? ? "C1'" A A 17 ? ? N9 A A 17 ? ? 115.26 108.50 6.76 0.70 N 128 6 "O4'" A C 18 ? ? "C1'" A C 18 ? ? N1 A C 18 ? ? 114.03 108.50 5.53 0.70 N 129 6 "O4'" A C 20 ? ? "C1'" A C 20 ? ? N1 A C 20 ? ? 114.52 108.50 6.02 0.70 N 130 6 "C1'" A U 21 ? ? "O4'" A U 21 ? ? "C4'" A U 21 ? ? 103.36 109.70 -6.34 0.70 N 131 6 "C1'" A C 22 ? ? "O4'" A C 22 ? ? "C4'" A C 22 ? ? 104.10 109.70 -5.60 0.70 N 132 6 "C3'" A G 23 ? ? "C2'" A G 23 ? ? "C1'" A G 23 ? ? 106.87 101.50 5.37 0.80 N 133 6 "O4'" A G 23 ? ? "C1'" A G 23 ? ? N9 A G 23 ? ? 113.62 108.50 5.12 0.70 N 134 6 "O4'" A U 24 ? ? "C1'" A U 24 ? ? N1 A U 24 ? ? 114.21 108.50 5.71 0.70 N 135 6 "O4'" A C 26 ? ? "C1'" A C 26 ? ? N1 A C 26 ? ? 114.96 108.50 6.46 0.70 N 136 6 "O4'" A C 27 ? ? "C1'" A C 27 ? ? N1 A C 27 ? ? 113.62 108.50 5.12 0.70 N 137 7 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 112.73 108.50 4.23 0.70 N 138 7 "C1'" A G 2 ? ? "O4'" A G 2 ? ? "C4'" A G 2 ? ? 104.06 109.70 -5.64 0.70 N 139 7 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.82 108.50 4.32 0.70 N 140 7 "O4'" A A 4 ? ? "C1'" A A 4 ? ? N9 A A 4 ? ? 113.38 108.50 4.88 0.70 N 141 7 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 113.49 108.50 4.99 0.70 N 142 7 "O4'" A G 6 ? ? "C1'" A G 6 ? ? N9 A G 6 ? ? 114.50 108.50 6.00 0.70 N 143 7 "C3'" A A 7 ? ? "C2'" A A 7 ? ? "C1'" A A 7 ? ? 106.61 101.50 5.11 0.80 N 144 7 "C3'" A A 7 ? ? "O3'" A A 7 ? ? P A G 8 ? ? 127.05 119.70 7.35 1.20 Y 145 7 "C1'" A G 8 ? ? "O4'" A G 8 ? ? "C4'" A G 8 ? ? 104.00 109.70 -5.70 0.70 N 146 7 "O4'" A G 8 ? ? "C1'" A G 8 ? ? "C2'" A G 8 ? ? 98.76 105.80 -7.04 1.00 N 147 7 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 115.41 108.50 6.91 0.70 N 148 7 "O4'" A A 13 ? ? "C1'" A A 13 ? ? N9 A A 13 ? ? 113.84 108.50 5.34 0.70 N 149 7 "C3'" A A 13 ? ? "O3'" A A 13 ? ? P A G 14 ? ? 126.93 119.70 7.23 1.20 Y 150 7 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 114.53 108.50 6.03 0.70 N 151 7 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 115.52 108.50 7.02 0.70 N 152 7 "O4'" A A 17 ? ? "C1'" A A 17 ? ? N9 A A 17 ? ? 112.75 108.50 4.25 0.70 N 153 7 N1 A A 17 ? ? C6 A A 17 ? ? N6 A A 17 ? ? 122.32 118.60 3.72 0.60 N 154 7 "O4'" A C 18 ? ? "C1'" A C 18 ? ? N1 A C 18 ? ? 113.34 108.50 4.84 0.70 N 155 7 "O4'" A C 20 ? ? "C1'" A C 20 ? ? N1 A C 20 ? ? 112.97 108.50 4.47 0.70 N 156 7 "C3'" A C 20 ? ? "O3'" A C 20 ? ? P A U 21 ? ? 130.39 119.70 10.69 1.20 Y 157 7 "C3'" A U 21 ? ? "O3'" A U 21 ? ? P A C 22 ? ? 129.93 119.70 10.23 1.20 Y 158 7 "C1'" A C 22 ? ? "O4'" A C 22 ? ? "C4'" A C 22 ? ? 102.97 109.70 -6.73 0.70 N 159 7 "O4'" A C 22 ? ? "C1'" A C 22 ? ? "C2'" A C 22 ? ? 98.11 105.80 -7.69 1.00 N 160 7 "O4'" A G 23 ? ? "C1'" A G 23 ? ? N9 A G 23 ? ? 116.05 108.50 7.55 0.70 N 161 7 "C3'" A G 23 ? ? "O3'" A G 23 ? ? P A U 24 ? ? 128.31 119.70 8.61 1.20 Y 162 7 "O4'" A U 24 ? ? "C1'" A U 24 ? ? N1 A U 24 ? ? 115.52 108.50 7.02 0.70 N 163 7 "O4'" A G 25 ? ? "C1'" A G 25 ? ? N9 A G 25 ? ? 112.86 108.50 4.36 0.70 N 164 7 "O4'" A C 26 ? ? "C1'" A C 26 ? ? N1 A C 26 ? ? 115.10 108.50 6.60 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1TOB 'double helix' 1TOB 'a-form double helix' 1TOB 'hairpin loop' 1TOB 'bulge loop' 1TOB 'mismatched base pair' # 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 G 1 1_555 A C 27 1_555 -0.664 -0.277 -0.061 6.767 3.324 -2.810 1 A_G1:C27_A A 1 ? A 27 ? 19 1 1 A G 2 1_555 A C 26 1_555 -0.803 -0.330 -0.173 -2.110 -13.546 1.376 2 A_G2:C26_A A 2 ? A 26 ? 19 1 1 A C 3 1_555 A G 25 1_555 0.711 -0.326 0.167 -7.166 -10.126 -2.606 3 A_C3:G25_A A 3 ? A 25 ? 19 1 1 A A 4 1_555 A U 24 1_555 0.316 0.005 0.371 9.768 -1.801 -5.091 4 A_A4:U24_A A 4 ? A 24 ? 20 1 1 A C 5 1_555 A G 23 1_555 0.648 -0.253 -0.376 18.214 -7.449 -1.809 5 A_C5:G23_A A 5 ? A 23 ? 19 1 1 A G 6 1_555 A C 22 1_555 -0.687 -0.357 -0.743 -17.953 -1.468 -1.904 6 A_G6:C22_A A 6 ? A 22 ? 19 1 1 A A 7 1_555 A U 21 1_555 0.148 -0.038 0.334 6.759 15.045 -3.952 7 A_A7:U21_A A 7 ? A 21 ? 20 1 1 A G 8 1_555 A C 20 1_555 -0.594 -0.296 -0.115 3.821 7.624 -2.389 8 A_G8:C20_A A 8 ? A 20 ? 19 1 1 A G 9 1_555 A C 18 1_555 -0.639 -0.253 -0.086 -10.524 2.081 -3.608 9 A_G9:C18_A A 9 ? A 18 ? 19 1 1 A U 10 1_555 A A 17 1_555 -0.218 -0.147 0.235 4.184 0.625 -4.689 10 A_U10:A17_A A 10 ? A 17 ? 20 1 1 A U 11 1_555 A U 16 1_555 2.940 -1.981 0.248 13.254 -15.297 14.577 11 A_U11:U16_A A 11 ? A 16 ? 16 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 G 1 1_555 A C 27 1_555 A G 2 1_555 A C 26 1_555 -0.217 -3.134 3.219 -3.878 10.550 24.938 -8.738 -0.312 1.782 22.997 8.452 27.318 1 AA_G1G2:C26C27_AA A 1 ? A 27 ? A 2 ? A 26 ? 1 A G 2 1_555 A C 26 1_555 A C 3 1_555 A G 25 1_555 -0.785 -1.305 3.291 -2.448 2.968 42.306 -2.102 0.835 3.234 4.102 3.383 42.473 2 AA_G2C3:G25C26_AA A 2 ? A 26 ? A 3 ? A 25 ? 1 A C 3 1_555 A G 25 1_555 A A 4 1_555 A U 24 1_555 -0.274 -1.258 2.553 -0.936 5.091 28.944 -3.297 0.390 2.310 10.083 1.854 29.394 3 AA_C3A4:U24G25_AA A 3 ? A 25 ? A 4 ? A 24 ? 1 A A 4 1_555 A U 24 1_555 A C 5 1_555 A G 23 1_555 0.791 -0.626 2.891 7.428 1.921 35.903 -1.233 -0.338 2.955 3.073 -11.883 36.687 4 AA_A4C5:G23U24_AA A 4 ? A 24 ? A 5 ? A 23 ? 1 A C 5 1_555 A G 23 1_555 A G 6 1_555 A C 22 1_555 0.297 -1.980 4.460 3.830 -4.159 21.053 -2.903 1.364 4.736 -11.126 -10.245 21.791 5 AA_C5G6:C22G23_AA A 5 ? A 23 ? A 6 ? A 22 ? 1 A G 6 1_555 A C 22 1_555 A A 7 1_555 A U 21 1_555 0.844 -1.933 2.506 -7.702 -9.115 32.361 -2.104 -2.406 2.673 -15.703 13.269 34.436 6 AA_G6A7:U21C22_AA A 6 ? A 22 ? A 7 ? A 21 ? 1 A A 7 1_555 A U 21 1_555 A G 8 1_555 A C 20 1_555 -1.745 -1.235 4.384 -5.387 -48.523 31.943 3.057 1.324 3.663 -58.413 6.484 57.802 7 AA_A7G8:C20U21_AA A 7 ? A 21 ? A 8 ? A 20 ? 1 A G 8 1_555 A C 20 1_555 A G 9 1_555 A C 18 1_555 2.008 -2.022 3.081 6.571 45.446 46.407 -3.410 -1.666 1.125 46.592 -6.736 64.377 8 AA_G8G9:C18C20_AA A 8 ? A 20 ? A 9 ? A 18 ? 1 A G 9 1_555 A C 18 1_555 A U 10 1_555 A A 17 1_555 0.244 -1.969 2.800 -1.738 -2.198 29.469 -3.447 -0.799 2.917 -4.308 3.406 29.599 9 AA_G9U10:A17C18_AA A 9 ? A 18 ? A 10 ? A 17 ? 1 A U 10 1_555 A A 17 1_555 A U 11 1_555 A U 16 1_555 0.601 -0.986 2.773 2.009 1.962 47.580 -1.353 -0.608 2.754 2.430 -2.488 47.658 10 AA_U10U11:U16A17_AA A 10 ? A 17 ? A 11 ? A 16 ? # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier TOA 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-Glcp3N TOC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-3-deoxy-GlcpN6N # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 3-ammonio-3-deoxy-alpha-D-glucopyranose TOA 3 2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose TOC 4 1,3-DIAMINO-5,6-DIHYDROXYCYCLOHEXANE TOB #