data_1NBK # _entry.id 1NBK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.396 _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 1NBK pdb_00001nbk 10.2210/pdb1nbk/pdb RCSB RCSB017743 ? ? WWPDB D_1000017743 ? ? # 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 2003-12-03 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 5 'Structure model' 1 4 2024-05-29 6 'Structure model' 1 5 2024-09-18 # _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 5 'Structure model' 'Data collection' 6 6 'Structure model' 'Source and taxonomy' 7 6 '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' database_2 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list 4 4 'Structure model' struct_site 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond 7 6 'Structure model' chem_comp 8 6 'Structure model' pdbx_entity_src_syn # 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' '_struct_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' 6 6 'Structure model' '_chem_comp.mon_nstd_flag' 7 6 'Structure model' '_chem_comp.pdbx_synonyms' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NBK _pdbx_database_status.recvd_initial_deposition_date 2002-12-03 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Matsugami, A.' 1 'Kobayashi, S.' 2 'Ouhashi, K.' 3 'Uesugi, S.' 4 'Yamamoto, R.' 5 'Taira, K.' 6 'Nishikawa, S.' 7 'Kumar, P.K.R.' 8 'Katahira, M.' 9 # _citation.id primary _citation.title 'Structural Basis of the Highly Efficient Trapping of the HIV Tat Protein by an RNA Aptamer' _citation.journal_abbrev Structure _citation.journal_volume 11 _citation.page_first 533 _citation.page_last 545 _citation.year 2003 _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 12737819 _citation.pdbx_database_id_DOI '10.1016/S0969-2126(03)00069-8' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Matsugami, A.' 1 ? primary 'Kobayashi, S.' 2 ? primary 'Ouhashi, K.' 3 ? primary 'Uesugi, S.' 4 ? primary 'Yamamoto, R.' 5 ? primary 'Taira, K.' 6 ? primary 'Nishikawa, S.' 7 ? primary 'Kumar, P.K.R.' 8 ? primary 'Katahira, M.' 9 ? # 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 aptamer' 10921.535 1 ? ? ? ? 2 non-polymer syn '2-AMINO-5-GUANIDINO-PENTANOIC ACID' 175.209 2 ? ? ? ? # _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 GGGAGCUUGAUCCCGGAAACGGUCGAUCGCUCCC _entity_poly.pdbx_seq_one_letter_code_can GGGAGCUUGAUCCCGGAAACGGUCGAUCGCUCCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name '2-AMINO-5-GUANIDINO-PENTANOIC ACID' _pdbx_entity_nonpoly.comp_id GND # 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 G n 1 4 A n 1 5 G n 1 6 C n 1 7 U n 1 8 U n 1 9 G n 1 10 A n 1 11 U n 1 12 C n 1 13 C n 1 14 C n 1 15 G n 1 16 G n 1 17 A n 1 18 A n 1 19 A n 1 20 C n 1 21 G n 1 22 G n 1 23 U n 1 24 C n 1 25 G n 1 26 A n 1 27 U n 1 28 C n 1 29 G n 1 30 C n 1 31 U n 1 32 C n 1 33 C n 1 34 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _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 ? # 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 GND 'L-peptide linking' n '2-AMINO-5-GUANIDINO-PENTANOIC ACID' 'L-argininium(2+); L-argininediium' 'C6 H15 N4 O2 1' 175.209 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 G 3 3 3 G G A . n A 1 4 A 4 4 4 A A A . n A 1 5 G 5 5 5 G G A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n A 1 10 A 10 10 10 A A A . n A 1 11 U 11 11 11 U U A . n A 1 12 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 G 15 15 15 G G A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A 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 G 21 21 21 G G A . n A 1 22 G 22 22 22 G G A . n A 1 23 U 23 23 23 U U A . n A 1 24 C 24 24 24 C C A . n A 1 25 G 25 25 25 G G A . n A 1 26 A 26 26 26 A A A . n A 1 27 U 27 27 27 U U A . n A 1 28 C 28 28 28 C C A . n A 1 29 G 29 29 29 G G A . n A 1 30 C 30 30 30 C C A . n A 1 31 U 31 31 31 U U A . n A 1 32 C 32 32 32 C C A . n A 1 33 C 33 33 33 C C A . n A 1 34 C 34 34 34 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 GND 1 35 35 GND ARG A . C 2 GND 1 36 36 GND ARG A . # _exptl.entry_id 1NBK _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 1NBK _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 1NBK _struct.title 'The structure of RNA aptamer for HIV Tat complexed with two argininamide molecules' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NBK _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA-LIGANDS COMPLEX, BASE TRIPLE, RNA APTAMER, HIV TAT, 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 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1NBK _struct_ref.pdbx_db_accession 1NBK _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1NBK _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 34 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1NBK _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 34 _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 34 # _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 # _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_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 34 N3 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 33 N3 ? ? A G 2 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 33 O2 ? ? A G 2 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 33 N4 ? ? A G 2 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 32 N3 ? ? A G 3 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 32 O2 ? ? A G 3 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 32 N4 ? ? A G 3 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 31 N3 ? ? A A 4 A U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 31 O4 ? ? A A 4 A U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 5 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 5 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 5 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 29 N1 ? ? A C 6 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 29 O6 ? ? A C 6 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 29 N2 ? ? A C 6 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 10 N7 ? ? A U 7 A A 10 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog19 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 10 N6 ? ? A U 7 A A 10 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 28 N3 ? ? A G 9 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 28 O2 ? ? A G 9 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 28 N4 ? ? A G 9 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 27 N3 ? ? A A 10 A U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 27 O4 ? ? A A 10 A U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 26 N1 ? ? A U 11 A A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 26 N6 ? ? A U 11 A A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 12 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 12 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 12 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 14 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 14 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 14 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 15 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 15 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 15 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 15 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 15 O6 ? ? ? 1_555 A C 20 N4 ? ? A G 15 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 15 N1 ? ? ? 1_555 A G 21 N3 ? ? A G 15 A G 21 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog40 hydrog ? ? A G 16 N2 ? ? ? 1_555 A A 19 N7 ? ? A G 16 A A 19 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog41 hydrog ? ? A G 16 N3 ? ? ? 1_555 A A 19 N6 ? ? A G 16 A A 19 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog42 hydrog ? ? A U 23 N3 ? ? ? 1_555 A A 26 N7 ? ? A U 23 A A 26 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog43 hydrog ? ? A U 23 O4 ? ? ? 1_555 A A 26 N6 ? ? A U 23 A A 26 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A GND 35 ? 6 'BINDING SITE FOR RESIDUE GND A 35' AC2 Software A GND 36 ? 7 'BINDING SITE FOR RESIDUE GND A 36' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 C A 6 ? C A 6 . ? 1_555 ? 2 AC1 6 U A 7 ? U A 7 . ? 1_555 ? 3 AC1 6 G A 9 ? G A 9 . ? 1_555 ? 4 AC1 6 U A 27 ? U A 27 . ? 1_555 ? 5 AC1 6 C A 28 ? C A 28 . ? 1_555 ? 6 AC1 6 G A 29 ? G A 29 . ? 1_555 ? 7 AC2 7 U A 7 ? U A 7 . ? 1_555 ? 8 AC2 7 A A 10 ? A A 10 . ? 1_555 ? 9 AC2 7 U A 11 ? U A 11 . ? 1_555 ? 10 AC2 7 C A 12 ? C A 12 . ? 1_555 ? 11 AC2 7 G A 22 ? G A 22 . ? 1_555 ? 12 AC2 7 U A 23 ? U A 23 . ? 1_555 ? 13 AC2 7 G A 25 ? G A 25 . ? 1_555 ? # 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 H21 A G 16 ? ? OP2 A A 19 ? ? 1.39 2 1 O6 A G 2 ? ? H41 A C 33 ? ? 1.42 3 1 N7 A G 25 ? ? HH22 A GND 36 ? ? 1.47 4 1 H41 A C 12 ? ? O6 A G 25 ? ? 1.48 5 1 H41 A C 6 ? ? O6 A G 29 ? ? 1.48 6 1 O6 A G 9 ? ? H41 A C 28 ? ? 1.51 7 1 O6 A G 15 ? ? H41 A C 20 ? ? 1.51 8 1 H41 A C 13 ? ? O6 A G 22 ? ? 1.53 9 1 "O2'" A A 26 ? ? "H5'" A U 27 ? ? 1.57 10 1 O6 A G 3 ? ? H41 A C 32 ? ? 1.58 # 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 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.66 113.10 4.56 0.50 N 2 1 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.72 106.40 -2.68 0.40 N 3 1 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.61 113.10 4.51 0.50 N 4 1 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.71 106.40 -2.69 0.40 N 5 1 N7 A G 3 ? ? C8 A G 3 ? ? N9 A G 3 ? ? 117.63 113.10 4.53 0.50 N 6 1 C8 A G 3 ? ? N9 A G 3 ? ? C4 A G 3 ? ? 103.76 106.40 -2.64 0.40 N 7 1 N7 A A 4 ? ? C8 A A 4 ? ? N9 A A 4 ? ? 117.51 113.80 3.71 0.50 N 8 1 N7 A G 5 ? ? C8 A G 5 ? ? N9 A G 5 ? ? 117.64 113.10 4.54 0.50 N 9 1 C8 A G 5 ? ? N9 A G 5 ? ? C4 A G 5 ? ? 103.78 106.40 -2.62 0.40 N 10 1 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.47 113.10 4.37 0.50 N 11 1 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.64 106.40 -2.76 0.40 N 12 1 N7 A A 10 ? ? C8 A A 10 ? ? N9 A A 10 ? ? 117.50 113.80 3.70 0.50 N 13 1 N7 A G 15 ? ? C8 A G 15 ? ? N9 A G 15 ? ? 117.66 113.10 4.56 0.50 N 14 1 C8 A G 15 ? ? N9 A G 15 ? ? C4 A G 15 ? ? 103.79 106.40 -2.61 0.40 N 15 1 N7 A G 16 ? ? C8 A G 16 ? ? N9 A G 16 ? ? 117.60 113.10 4.50 0.50 N 16 1 C8 A G 16 ? ? N9 A G 16 ? ? C4 A G 16 ? ? 103.77 106.40 -2.63 0.40 N 17 1 N7 A A 17 ? ? C8 A A 17 ? ? N9 A A 17 ? ? 117.60 113.80 3.80 0.50 N 18 1 N7 A A 18 ? ? C8 A A 18 ? ? N9 A A 18 ? ? 117.64 113.80 3.84 0.50 N 19 1 N7 A A 19 ? ? C8 A A 19 ? ? N9 A A 19 ? ? 117.65 113.80 3.85 0.50 N 20 1 N7 A G 21 ? ? C8 A G 21 ? ? N9 A G 21 ? ? 117.62 113.10 4.52 0.50 N 21 1 C8 A G 21 ? ? N9 A G 21 ? ? C4 A G 21 ? ? 103.78 106.40 -2.62 0.40 N 22 1 N7 A G 22 ? ? C8 A G 22 ? ? N9 A G 22 ? ? 117.69 113.10 4.59 0.50 N 23 1 C8 A G 22 ? ? N9 A G 22 ? ? C4 A G 22 ? ? 103.78 106.40 -2.62 0.40 N 24 1 N7 A G 25 ? ? C8 A G 25 ? ? N9 A G 25 ? ? 117.64 113.10 4.54 0.50 N 25 1 C8 A G 25 ? ? N9 A G 25 ? ? C4 A G 25 ? ? 103.70 106.40 -2.70 0.40 N 26 1 N7 A A 26 ? ? C8 A A 26 ? ? N9 A A 26 ? ? 117.50 113.80 3.70 0.50 N 27 1 N7 A G 29 ? ? C8 A G 29 ? ? N9 A G 29 ? ? 117.65 113.10 4.55 0.50 N 28 1 C8 A G 29 ? ? N9 A G 29 ? ? C4 A G 29 ? ? 103.72 106.40 -2.68 0.40 N # _pdbx_nmr_ensemble.entry_id 1NBK _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 1NBK _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '1.7mM RNA U-15N,13C; 6.8mM argininamide; 10mM sodium phosphate buffer; 30mM NaCl; 0.1mM EDTA' '95% H2O/5% D2O' ? ? ? 2 '1.7mM RNA U-15N,13C; 6.8mM argininamide; 10mM sodium phosphate buffer; 30mM NaCl; 0.1mM EDTA' '100% D2O' ? ? ? 3 '1.7mM RNA; 6.8mM argininamide; 10mM sodium phosphate buffer; 30mM NaCl; 0.1mM EDTA' '95% H2O/5% D2O' ? ? ? 4 '1.7mM RNA; 6.8mM argininamide; 10mM sodium phosphate buffer; 30mM NaCl; 0.1mM EDTA' '100% 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 _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 1 278 ambient 6.7 ? ? K ? ? ? 2 308 ambient 6.7 ? ? K ? ? ? # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 3D_15N-separated_NOESY 2 2 2 3D_13C-separated_NOESY 3 3 1 '2D NOESY' 4 4 2 '2D NOESY' 5 4 2 '2D TOCSY' 6 4 2 DQF-COSY 7 4 2 '1H-31P HetCor' 8 2 2 'spin echo difference CT 1H-13C HSQC' 9 1 1 HNN-COSY 10 2 2 HNN-COSY # _pdbx_nmr_refine.entry_id 1NBK _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _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 X-PLOR 3.851 'structure solution' Brunger 1 X-PLOR 3.851 refinement Brunger 2 # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 GND CA C N S 111 GND CB C N N 112 GND CG C N N 113 GND CD C N N 114 GND NE N N N 115 GND CZ C N N 116 GND NH1 N N N 117 GND NH2 N N N 118 GND C C N N 119 GND OXT O N N 120 GND O O N N 121 GND N N N N 122 GND HA H N N 123 GND HB1 H N N 124 GND HB2 H N N 125 GND HG1 H N N 126 GND HG2 H N N 127 GND HD1 H N N 128 GND HD2 H N N 129 GND HE H N N 130 GND HH11 H N N 131 GND HH21 H N N 132 GND HH22 H N N 133 GND HXT H N N 134 GND HN1 H N N 135 GND HN2 H N N 136 GND HN3 H N N 137 U OP3 O N N 138 U P P N N 139 U OP1 O N N 140 U OP2 O N N 141 U "O5'" O N N 142 U "C5'" C N N 143 U "C4'" C N R 144 U "O4'" O N N 145 U "C3'" C N S 146 U "O3'" O N N 147 U "C2'" C N R 148 U "O2'" O N N 149 U "C1'" C N R 150 U N1 N N N 151 U C2 C N N 152 U O2 O N N 153 U N3 N N N 154 U C4 C N N 155 U O4 O N N 156 U C5 C N N 157 U C6 C N N 158 U HOP3 H N N 159 U HOP2 H N N 160 U "H5'" H N N 161 U "H5''" H N N 162 U "H4'" H N N 163 U "H3'" H N N 164 U "HO3'" H N N 165 U "H2'" H N N 166 U "HO2'" H N N 167 U "H1'" H N N 168 U H3 H N N 169 U H5 H N N 170 U H6 H N N 171 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 GND CA CB sing N N 116 GND CA C sing N N 117 GND CA N sing N N 118 GND CA HA sing N N 119 GND CB CG sing N N 120 GND CB HB1 sing N N 121 GND CB HB2 sing N N 122 GND CG CD sing N N 123 GND CG HG1 sing N N 124 GND CG HG2 sing N N 125 GND CD NE sing N N 126 GND CD HD1 sing N N 127 GND CD HD2 sing N N 128 GND NE CZ sing N N 129 GND NE HE sing N N 130 GND CZ NH1 doub N N 131 GND CZ NH2 sing N N 132 GND NH1 HH11 sing N N 133 GND NH2 HH21 sing N N 134 GND NH2 HH22 sing N N 135 GND C OXT sing N N 136 GND C O doub N N 137 GND OXT HXT sing N N 138 GND N HN1 sing N N 139 GND N HN2 sing N N 140 GND N HN3 sing N N 141 U OP3 P sing N N 142 U OP3 HOP3 sing N N 143 U P OP1 doub N N 144 U P OP2 sing N N 145 U P "O5'" sing N N 146 U OP2 HOP2 sing N N 147 U "O5'" "C5'" sing N N 148 U "C5'" "C4'" sing N N 149 U "C5'" "H5'" sing N N 150 U "C5'" "H5''" sing N N 151 U "C4'" "O4'" sing N N 152 U "C4'" "C3'" sing N N 153 U "C4'" "H4'" sing N N 154 U "O4'" "C1'" sing N N 155 U "C3'" "O3'" sing N N 156 U "C3'" "C2'" sing N N 157 U "C3'" "H3'" sing N N 158 U "O3'" "HO3'" sing N N 159 U "C2'" "O2'" sing N N 160 U "C2'" "C1'" sing N N 161 U "C2'" "H2'" sing N N 162 U "O2'" "HO2'" sing N N 163 U "C1'" N1 sing N N 164 U "C1'" "H1'" sing N N 165 U N1 C2 sing N N 166 U N1 C6 sing N N 167 U C2 O2 doub N N 168 U C2 N3 sing N N 169 U N3 C4 sing N N 170 U N3 H3 sing N N 171 U C4 O4 doub N N 172 U C4 C5 sing N N 173 U C5 C6 doub N N 174 U C5 H5 sing N N 175 U C6 H6 sing N N 176 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1NBK 'double helix' 1NBK 'a-form double helix' 1NBK tetraloop 1NBK 'bulge loop' 1NBK '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 34 1_555 -0.068 0.043 0.336 4.019 -1.217 -3.324 1 A_G1:C34_A A 1 ? A 34 ? 19 1 1 A G 2 1_555 A C 33 1_555 -0.093 -0.338 0.079 -0.026 -2.743 -9.481 2 A_G2:C33_A A 2 ? A 33 ? 19 1 1 A G 3 1_555 A C 32 1_555 0.452 -0.186 -0.803 -13.348 -3.025 -14.224 3 A_G3:C32_A A 3 ? A 32 ? 19 1 1 A A 4 1_555 A U 31 1_555 0.861 0.110 0.258 9.392 6.216 -10.397 4 A_A4:U31_A A 4 ? A 31 ? 20 1 1 A G 5 1_555 A C 30 1_555 0.600 -0.136 -0.399 5.522 -1.224 -0.730 5 A_G5:C30_A A 5 ? A 30 ? 19 1 1 A C 6 1_555 A G 29 1_555 0.636 -0.535 0.006 10.335 -11.134 -10.815 6 A_C6:G29_A A 6 ? A 29 ? 19 1 1 A G 9 1_555 A C 28 1_555 -0.284 -0.344 0.268 0.035 -2.691 -9.242 7 A_G9:C28_A A 9 ? A 28 ? 19 1 1 A A 10 1_555 A U 27 1_555 -0.052 -0.253 -0.007 17.705 3.601 3.553 8 A_A10:U27_A A 10 ? A 27 ? 20 1 1 A U 11 1_555 A A 26 1_555 -0.580 -0.067 -0.025 -0.559 -0.866 -0.874 9 A_U11:A26_A A 11 ? A 26 ? 20 1 1 A C 12 1_555 A G 25 1_555 -0.156 -0.234 -0.148 0.424 -1.160 -10.028 10 A_C12:G25_A A 12 ? A 25 ? 19 1 1 A C 13 1_555 A G 22 1_555 0.706 -0.821 -0.741 -12.621 -19.756 1.077 11 A_C13:G22_A A 13 ? A 22 ? 19 1 1 A C 14 1_555 A G 21 1_555 -0.077 -0.007 0.348 -10.232 12.854 0.095 12 A_C14:G21_A A 14 ? A 21 ? 19 1 1 A G 15 1_555 A C 20 1_555 -0.141 -0.373 -0.159 45.560 28.313 -13.307 13 A_G15:C20_A A 15 ? A 20 ? 19 1 1 A G 16 1_555 A A 19 1_555 6.810 -4.793 0.201 6.972 -28.147 -18.262 14 A_G16:A19_A A 16 ? A 19 ? 11 10 # 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 34 1_555 A G 2 1_555 A C 33 1_555 -1.822 -1.133 3.626 -11.718 19.101 45.964 -2.817 1.202 3.291 22.929 14.067 50.868 1 AA_G1G2:C33C34_AA A 1 ? A 34 ? A 2 ? A 33 ? 1 A G 2 1_555 A C 33 1_555 A G 3 1_555 A C 32 1_555 0.083 -2.917 4.068 5.749 21.332 22.743 -8.963 0.821 1.018 43.175 -11.635 31.605 2 AA_G2G3:C32C33_AA A 2 ? A 33 ? A 3 ? A 32 ? 1 A G 3 1_555 A C 32 1_555 A A 4 1_555 A U 31 1_555 0.942 -1.153 2.730 -0.671 -15.787 40.709 -0.183 -1.328 2.946 -21.731 0.923 43.547 3 AA_G3A4:U31C32_AA A 3 ? A 32 ? A 4 ? A 31 ? 1 A A 4 1_555 A U 31 1_555 A G 5 1_555 A C 30 1_555 -0.501 -1.848 3.765 5.769 7.485 20.824 -7.436 3.401 2.712 19.467 -15.005 22.847 4 AA_A4G5:C30U31_AA A 4 ? A 31 ? A 5 ? A 30 ? 1 A G 5 1_555 A C 30 1_555 A C 6 1_555 A G 29 1_555 -0.861 -1.436 3.020 -3.484 9.483 35.114 -3.449 0.951 2.628 15.329 5.633 36.495 5 AA_G5C6:G29C30_AA A 5 ? A 30 ? A 6 ? A 29 ? 1 A C 6 1_555 A G 29 1_555 A G 9 1_555 A C 28 1_555 -2.811 -1.888 3.327 4.162 11.143 54.019 -2.651 3.262 2.712 12.103 -4.520 55.217 6 AA_C6G9:C28G29_AA A 6 ? A 29 ? A 9 ? A 28 ? 1 A G 9 1_555 A C 28 1_555 A A 10 1_555 A U 27 1_555 0.310 -1.096 3.015 -0.920 0.526 18.491 -3.668 -1.419 2.964 1.636 2.859 18.521 7 AA_G9A10:U27C28_AA A 9 ? A 28 ? A 10 ? A 27 ? 1 A A 10 1_555 A U 27 1_555 A U 11 1_555 A A 26 1_555 -0.663 -2.188 4.762 -1.203 -12.146 34.472 -0.848 0.796 5.232 -19.745 1.955 36.507 8 AA_A10U11:A26U27_AA A 10 ? A 27 ? A 11 ? A 26 ? 1 A U 11 1_555 A A 26 1_555 A C 12 1_555 A G 25 1_555 0.349 -1.779 3.151 -2.839 11.968 25.169 -6.067 -1.288 2.057 25.604 6.073 27.970 9 AA_U11C12:G25A26_AA A 11 ? A 26 ? A 12 ? A 25 ? 1 A C 12 1_555 A G 25 1_555 A C 13 1_555 A G 22 1_555 2.536 -1.450 3.691 -5.048 17.974 62.931 -2.123 -2.567 3.034 16.828 4.727 65.368 10 AA_C12C13:G22G25_AA A 12 ? A 25 ? A 13 ? A 22 ? 1 A C 13 1_555 A G 22 1_555 A C 14 1_555 A G 21 1_555 -0.041 -1.015 3.051 -5.231 27.564 21.982 -4.903 -0.547 1.136 51.731 9.818 35.506 11 AA_C13C14:G21G22_AA A 13 ? A 22 ? A 14 ? A 21 ? 1 A C 14 1_555 A G 21 1_555 A G 15 1_555 A C 20 1_555 -0.497 -0.994 2.127 -4.058 -8.877 26.754 -0.577 0.350 2.376 -18.423 8.421 28.448 12 AA_C14G15:C20G21_AA A 14 ? A 21 ? A 15 ? A 20 ? 1 A G 15 1_555 A C 20 1_555 A G 16 1_555 A A 19 1_555 -2.275 -1.214 6.065 -1.398 5.840 50.840 -2.149 2.456 5.957 6.775 1.622 51.170 13 AA_G15G16:A19C20_AA A 15 ? A 20 ? A 16 ? A 19 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DRX _pdbx_nmr_spectrometer.field_strength 600 # _atom_sites.entry_id 1NBK _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_