data_1QD3 # _entry.id 1QD3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 1QD3 pdb_00001qd3 10.2210/pdb1qd3/pdb RCSB RCSB001219 ? ? WWPDB D_1000001219 ? ? # 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 2000-07-12 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2020-07-29 5 'Structure model' 2 1 2023-12-27 # 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 4 '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' Advisory 4 4 'Structure model' 'Atomic model' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Structure summary' 8 5 'Structure model' 'Data collection' 9 5 'Structure model' 'Database references' 10 5 'Structure model' 'Derived calculations' 11 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' atom_site 2 4 'Structure model' chem_comp 3 4 'Structure model' database_PDB_caveat 4 4 'Structure model' entity 5 4 'Structure model' pdbx_branch_scheme 6 4 'Structure model' pdbx_chem_comp_identifier 7 4 'Structure model' pdbx_entity_branch 8 4 'Structure model' pdbx_entity_branch_descriptor 9 4 'Structure model' pdbx_entity_branch_link 10 4 'Structure model' pdbx_entity_branch_list 11 4 'Structure model' pdbx_entity_nonpoly 12 4 'Structure model' pdbx_nmr_software 13 4 'Structure model' pdbx_nonpoly_scheme 14 4 'Structure model' pdbx_struct_assembly 15 4 'Structure model' pdbx_struct_oper_list 16 4 'Structure model' pdbx_validate_chiral 17 4 'Structure model' struct_asym 18 4 'Structure model' struct_conn 19 4 'Structure model' struct_site 20 4 'Structure model' struct_site_gen 21 5 'Structure model' chem_comp 22 5 'Structure model' chem_comp_atom 23 5 'Structure model' chem_comp_bond 24 5 'Structure model' database_2 25 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_atom_site.B_iso_or_equiv' 2 4 'Structure model' '_atom_site.Cartn_x' 3 4 'Structure model' '_atom_site.Cartn_y' 4 4 'Structure model' '_atom_site.Cartn_z' 5 4 'Structure model' '_atom_site.auth_asym_id' 6 4 'Structure model' '_atom_site.auth_atom_id' 7 4 'Structure model' '_atom_site.auth_comp_id' 8 4 'Structure model' '_atom_site.auth_seq_id' 9 4 'Structure model' '_atom_site.label_asym_id' 10 4 'Structure model' '_atom_site.label_atom_id' 11 4 'Structure model' '_atom_site.label_comp_id' 12 4 'Structure model' '_atom_site.label_entity_id' 13 4 'Structure model' '_atom_site.type_symbol' 14 4 'Structure model' '_chem_comp.name' 15 4 'Structure model' '_chem_comp.type' 16 4 'Structure model' '_pdbx_nmr_software.name' 17 4 'Structure model' '_struct_conn.pdbx_dist_value' 18 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 19 4 'Structure model' '_struct_conn.pdbx_value_order' 20 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 28 5 'Structure model' '_chem_comp.pdbx_synonyms' 29 5 'Structure model' '_database_2.pdbx_DOI' 30 5 'Structure model' '_database_2.pdbx_database_accession' 31 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _database_PDB_caveat.id 1 _database_PDB_caveat.text 'RIB B 1 HAS WRONG CHIRALITY AT ATOM C1' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1QD3 _pdbx_database_status.recvd_initial_deposition_date 1999-07-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 'Faber, C.' 1 'Sticht, H.' 2 'Roesch, P.' 3 # 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 'Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B.' J.Biol.Chem. 275 20660 20666 2000 JBCHA3 US 0021-9258 0071 ? 10747964 10.1074/jbc.M000920200 1 'Binding of Neomycin to the Tar Element of HIV-1 RNA Induces Dissociation of Tat Protein by an Allosteric Mechanism' Biochemistry 37 5549 ? 1998 BICHAW US 0006-2960 0033 ? ? 10.1021/bi972808a # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Faber, C.' 1 ? primary 'Sticht, H.' 2 ? primary 'Schweimer, K.' 3 ? primary 'Rosch, P.' 4 ? 1 'Wang, S.' 5 ? 1 'Huber, P.W.' 6 ? 1 'Mei, C.' 7 ? 1 'Czarnik, A.W.' 8 ? 1 'Mei, H.Y.' 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 nat 'HIV-1 TAR RNA' 9308.538 1 ? ? 'RESIDUES 17-45' 'NEOMYCIN B (RESIDUES BDG-CYY-RYB-IDG) COMPLEXED IN THE RNA MINOR GROOVE' 2 branched man '2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-alpha-D-ribofuranose' 310.301 1 ? ? ? ? 3 non-polymer man 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose 178.186 1 ? ? ? ? 4 non-polymer syn 2-DEOXYSTREPTAMINE 162.187 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 GCCAGAUUUGAGCCUGGGAGCUCUCUGGC _entity_poly.pdbx_seq_one_letter_code_can GCCAGAUUUGAGCCUGGGAGCUCUCUGGC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose BDG 4 2-DEOXYSTREPTAMINE CYY # 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 C n 1 3 C n 1 4 A n 1 5 G n 1 6 A n 1 7 U n 1 8 U n 1 9 U n 1 10 G n 1 11 A n 1 12 G n 1 13 C n 1 14 C n 1 15 U n 1 16 G n 1 17 G n 1 18 G n 1 19 A n 1 20 G n 1 21 C n 1 22 U n 1 23 C n 1 24 U n 1 25 C n 1 26 U n 1 27 G n 1 28 G n 1 29 C n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num ? _entity_src_nat.pdbx_end_seq_num ? _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Human immunodeficiency virus 1' _entity_src_nat.pdbx_ncbi_taxonomy_id 11676 _entity_src_nat.genus Lentivirus _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line 'Z2/CDC-Z34 ISOLATE' _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 2 'WURCS=2.0/2,2,1/[a222h-1a_1-4][a2121h-1b_1-5_2*N_6*N]/1-2/a3-b1' WURCS PDB2Glycan 1.1.0 2 2 '[][D-1-deoxy-Ribf]{[(3+1)][b-L-IdopN6N]{}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 IDG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 RIB _pdbx_entity_branch_link.atom_id_2 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.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 BDG 'D-saccharide, alpha linking' . 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose ;O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE; 2,6-diamino-2,6-dideoxy-alpha-D-glucose; 2,6-diamino-2,6-dideoxy-D-glucose; 2,6-diamino-2,6-dideoxy-glucose ; 'C6 H14 N2 O4' 178.186 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CYY non-polymer . 2-DEOXYSTREPTAMINE ? 'C6 H14 N2 O3' 162.187 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 IDG 'L-saccharide, beta linking' . 2,6-diamino-2,6-dideoxy-beta-L-idopyranose ;O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE; 2,6-diamino-2,6-dideoxy-beta-L-idose; 2,6-diamino-2,6-dideoxy-L-idose; 2,6-diamino-2,6-dideoxy-idose ; 'C6 H14 N2 O4' 178.186 RIB 'D-saccharide, alpha linking' . alpha-D-ribofuranose 'alpha-D-ribose; D-ribose; ribose' 'C5 H10 O5' 150.130 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 BDG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 'DGlcpN[6N]a' BDG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-GlcpN6N IDG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-L-IdopN6N RIB 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DRibfa RIB 'COMMON NAME' GMML 1.0 a-D-ribofuranose RIB 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-Ribf RIB 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Rib # 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 17 17 G G A . n A 1 2 C 2 18 18 C C A . n A 1 3 C 3 19 19 C C A . n A 1 4 A 4 20 20 A A A . n A 1 5 G 5 21 21 G G A . n A 1 6 A 6 22 22 A A A . n A 1 7 U 7 23 23 U U A . n A 1 8 U 8 24 24 U U A . n A 1 9 U 9 25 25 U U A . n A 1 10 G 10 26 26 G G A . n A 1 11 A 11 27 27 A A A . n A 1 12 G 12 28 28 G G A . n A 1 13 C 13 29 29 C C A . n A 1 14 C 14 30 30 C C A . n A 1 15 U 15 31 31 U U A . n A 1 16 G 16 32 32 G G A . n A 1 17 G 17 33 33 G G A . n A 1 18 G 18 34 34 G G A . n A 1 19 A 19 35 35 A A A . n A 1 20 G 20 36 36 G G A . n A 1 21 C 21 37 37 C C A . n A 1 22 U 22 38 38 U U A . n A 1 23 C 23 39 39 C C A . n A 1 24 U 24 40 40 U U A . n A 1 25 C 25 41 41 C C A . n A 1 26 U 26 42 42 U U A . n A 1 27 G 27 43 43 G G A . n A 1 28 G 28 44 44 G G A . n A 1 29 C 29 45 45 C C A . n # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero B 2 RIB 1 B RIB 1 ? RIB 48 n B 2 IDG 2 B IDG 2 ? IDG 49 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 C 3 BDG 1 46 46 BDG BDG A . D 4 CYY 1 47 47 CYY CYY A . # _cell.entry_id 1QD3 _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 1QD3 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 1QD3 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 1QD3 _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 1QD3 _struct.title 'HIV-1 TAR RNA/NEOMYCIN B COMPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1QD3 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HIV-1, AMINOGLYCOSIDE-RNA-COMPLEX, MINOR GROOVE BINDING, 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1QD3 _struct_ref.pdbx_db_accession 1QD3 _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 1QD3 _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 29 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1QD3 _struct_ref_seq.db_align_beg 17 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 45 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 17 _struct_ref_seq.pdbx_auth_seq_align_end 45 # _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 x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 # 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 ? C BDG . O1 ? ? ? 1_555 D CYY . C4 ? ? A BDG 46 A CYY 47 1_555 ? ? ? ? ? ? ? 1.452 ? ? covale2 covale one ? D CYY . O5 ? ? ? 1_555 B RIB . C1 ? ? A CYY 47 B RIB 1 1_555 ? ? ? ? ? ? ? 1.457 ? ? covale3 covale both ? B RIB . O3 ? ? ? 1_555 B IDG . C1 ? ? B RIB 1 B IDG 2 1_555 ? ? ? ? ? ? ? 1.443 sing ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 17 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 17 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 17 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 28 N1 ? ? A C 18 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 28 O6 ? ? A C 18 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 28 N2 ? ? A C 18 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 27 N1 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 27 O6 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 27 N2 ? ? A C 19 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 26 N3 ? ? A A 20 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 26 O4 ? ? A A 20 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 25 N3 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 25 O2 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 25 N4 ? ? A G 21 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 24 N3 ? ? A A 22 A U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 24 O4 ? ? A A 22 A U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 26 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 11 N1 ? ? ? 1_555 A U 22 N3 ? ? A A 27 A U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 11 N6 ? ? ? 1_555 A U 22 O4 ? ? A A 27 A U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 28 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 29 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 18 N1 ? ? A C 30 A G 34 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 U 42 ? ? "O5'" A G 43 ? ? 1.41 2 1 H61 A A 22 ? ? O4 A U 40 ? ? 1.50 3 1 "HO2'" A U 25 ? ? "O3'" A G 26 ? ? 1.55 4 2 H61 A A 22 ? ? O4 A U 40 ? ? 1.40 5 2 "HO2'" A U 42 ? ? "O5'" A G 43 ? ? 1.43 6 2 "HO2'" A A 22 ? ? "O5'" A U 23 ? ? 1.44 7 4 "HO2'" A A 22 ? ? "O5'" A U 23 ? ? 1.39 8 5 "O2'" A A 22 ? ? "HO2'" A U 23 ? ? 1.39 9 5 N1 A A 22 ? ? H3 A U 40 ? ? 1.59 10 6 "HO2'" A U 25 ? ? "O3'" A G 26 ? ? 1.50 11 6 H61 A A 22 ? ? O4 A U 40 ? ? 1.57 12 6 H21 A G 21 ? ? O2 A C 41 ? ? 1.57 13 6 "O2'" A A 22 ? ? "HO2'" A U 23 ? ? 1.58 14 8 "HO2'" A A 27 ? ? "O5'" A G 28 ? ? 1.49 15 9 "HO2'" A U 23 ? ? "O5'" A U 24 ? ? 1.46 16 9 H61 A A 22 ? ? O4 A U 40 ? ? 1.48 17 9 N1 A A 22 ? ? H3 A U 40 ? ? 1.53 18 9 H21 A G 21 ? ? O2 A C 41 ? ? 1.57 19 10 N1 A A 22 ? ? H3 A U 40 ? ? 1.44 20 10 O2 A C 30 ? ? H1 A G 34 ? ? 1.48 21 10 H21 A G 21 ? ? O2 A C 41 ? ? 1.56 22 11 "HO2'" A U 25 ? ? "O5'" A G 26 ? ? 1.42 23 11 H61 A A 22 ? ? O4 A U 40 ? ? 1.55 24 11 H21 A G 21 ? ? O2 A C 41 ? ? 1.56 25 13 "HO2'" A U 23 ? ? "O5'" A U 24 ? ? 1.50 26 14 "HO2'" A U 42 ? ? "O5'" A G 43 ? ? 1.45 27 14 "HO2'" A C 29 ? ? "O5'" A C 30 ? ? 1.50 28 14 "O2'" A A 22 ? ? "HO2'" A U 23 ? ? 1.52 29 14 H61 A A 22 ? ? O4 A U 40 ? ? 1.57 30 15 "HO2'" A A 22 ? ? "O5'" A U 23 ? ? 1.58 31 16 "O2'" A A 22 ? ? "HO2'" A U 23 ? ? 1.26 32 17 "O2'" A A 22 ? ? "HO2'" A U 23 ? ? 1.41 33 17 H61 A A 22 ? ? O4 A U 40 ? ? 1.48 # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 C1 ? B RIB 1 ? 'WRONG HAND' . 2 2 C1 ? B RIB 1 ? 'WRONG HAND' . 3 3 C1 ? B RIB 1 ? PLANAR . 4 13 C1 ? B RIB 1 ? PLANAR . 5 14 C1 ? B RIB 1 ? 'WRONG HAND' . # _pdbx_nmr_ensemble.entry_id 1QD3 _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 17 _pdbx_nmr_ensemble.conformer_selection_criteria 'LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents D2O _pdbx_nmr_sample_details.solvent_system ? # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 308 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6.4 _pdbx_nmr_exptl_sample_conditions.ionic_strength '110 mM' _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 COSY 1 3 1 TOCSY 1 4 1 HSQC-NOESY 1 5 1 HCCH-COSY 1 6 1 HCCH-TOCSY 1 7 1 XFILTERED-NOESY 1 # _pdbx_nmr_refine.entry_id 1QD3 _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details 'REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.' _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR 3.851 BRUNGER 1 'structure solution' NDEE ? ? 2 'structure solution' Xndee ? ? 3 'structure solution' XPLOR ? ? 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 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 BDG C5 C N R 38 BDG O5 O N N 39 BDG C1 C N S 40 BDG O1 O N N 41 BDG C2 C N R 42 BDG N2 N N N 43 BDG C3 C N R 44 BDG O3 O N N 45 BDG C4 C N S 46 BDG O4 O N N 47 BDG C6 C N N 48 BDG N6 N N N 49 BDG H5 H N N 50 BDG H1 H N N 51 BDG HO1 H N N 52 BDG H2 H N N 53 BDG HN21 H N N 54 BDG HN22 H N N 55 BDG H3 H N N 56 BDG HO3 H N N 57 BDG H4 H N N 58 BDG HO4 H N N 59 BDG H61 H N N 60 BDG H62 H N N 61 BDG HN61 H N N 62 BDG HN62 H N N 63 C OP3 O N N 64 C P P N N 65 C OP1 O N N 66 C OP2 O N N 67 C "O5'" O N N 68 C "C5'" C N N 69 C "C4'" C N R 70 C "O4'" O N N 71 C "C3'" C N S 72 C "O3'" O N N 73 C "C2'" C N R 74 C "O2'" O N N 75 C "C1'" C N R 76 C N1 N N N 77 C C2 C N N 78 C O2 O N N 79 C N3 N N N 80 C C4 C N N 81 C N4 N N N 82 C C5 C N N 83 C C6 C N N 84 C HOP3 H N N 85 C HOP2 H N N 86 C "H5'" H N N 87 C "H5''" H N N 88 C "H4'" H N N 89 C "H3'" H N N 90 C "HO3'" H N N 91 C "H2'" H N N 92 C "HO2'" H N N 93 C "H1'" H N N 94 C H41 H N N 95 C H42 H N N 96 C H5 H N N 97 C H6 H N N 98 CYY C1 C N R 99 CYY C2 C N N 100 CYY C3 C N S 101 CYY C4 C N R 102 CYY C5 C N S 103 CYY C6 C N S 104 CYY N1 N N N 105 CYY N3 N N N 106 CYY O4 O N N 107 CYY O5 O N N 108 CYY O6 O N N 109 CYY H1 H N N 110 CYY H21 H N N 111 CYY H22 H N N 112 CYY H3 H N N 113 CYY H4 H N N 114 CYY H5 H N N 115 CYY H6 H N N 116 CYY HN11 H N N 117 CYY HN12 H N N 118 CYY HN31 H N N 119 CYY HN32 H N N 120 CYY HO4 H N N 121 CYY HO5 H N N 122 CYY HO6 H N N 123 G OP3 O N N 124 G P P N N 125 G OP1 O N N 126 G OP2 O N N 127 G "O5'" O N N 128 G "C5'" C N N 129 G "C4'" C N R 130 G "O4'" O N N 131 G "C3'" C N S 132 G "O3'" O N N 133 G "C2'" C N R 134 G "O2'" O N N 135 G "C1'" C N R 136 G N9 N Y N 137 G C8 C Y N 138 G N7 N Y N 139 G C5 C Y N 140 G C6 C N N 141 G O6 O N N 142 G N1 N N N 143 G C2 C N N 144 G N2 N N N 145 G N3 N N N 146 G C4 C Y N 147 G HOP3 H N N 148 G HOP2 H N N 149 G "H5'" H N N 150 G "H5''" H N N 151 G "H4'" H N N 152 G "H3'" H N N 153 G "HO3'" H N N 154 G "H2'" H N N 155 G "HO2'" H N N 156 G "H1'" H N N 157 G H8 H N N 158 G H1 H N N 159 G H21 H N N 160 G H22 H N N 161 IDG C5 C N S 162 IDG O5 O N N 163 IDG C1 C N S 164 IDG O1 O N N 165 IDG C2 C N R 166 IDG N2 N N N 167 IDG C3 C N R 168 IDG O3 O N N 169 IDG C4 C N S 170 IDG O4 O N N 171 IDG C6 C N N 172 IDG N6 N N N 173 IDG H5 H N N 174 IDG H1 H N N 175 IDG HO1 H N N 176 IDG H2 H N N 177 IDG HN21 H N N 178 IDG HN22 H N N 179 IDG H3 H N N 180 IDG HO3 H N N 181 IDG H4 H N N 182 IDG HO4 H N N 183 IDG H61 H N N 184 IDG H62 H N N 185 IDG HN61 H N N 186 IDG HN62 H N N 187 RIB O5 O N N 188 RIB C5 C N N 189 RIB C4 C N R 190 RIB O4 O N N 191 RIB C3 C N S 192 RIB O3 O N N 193 RIB C2 C N R 194 RIB O2 O N N 195 RIB C1 C N S 196 RIB O1 O N N 197 RIB HO5 H N N 198 RIB H51 H N N 199 RIB H52 H N N 200 RIB H4 H N N 201 RIB H3 H N N 202 RIB HO3 H N N 203 RIB H2 H N N 204 RIB HO2 H N N 205 RIB H1 H N N 206 RIB HO1 H N N 207 U OP3 O N N 208 U P P N N 209 U OP1 O N N 210 U OP2 O N N 211 U "O5'" O N N 212 U "C5'" C N N 213 U "C4'" C N R 214 U "O4'" O N N 215 U "C3'" C N S 216 U "O3'" O N N 217 U "C2'" C N R 218 U "O2'" O N N 219 U "C1'" C N R 220 U N1 N N N 221 U C2 C N N 222 U O2 O N N 223 U N3 N N N 224 U C4 C N N 225 U O4 O N N 226 U C5 C N N 227 U C6 C N N 228 U HOP3 H N N 229 U HOP2 H N N 230 U "H5'" H N N 231 U "H5''" H N N 232 U "H4'" H N N 233 U "H3'" H N N 234 U "HO3'" H N N 235 U "H2'" H N N 236 U "HO2'" H N N 237 U "H1'" H N N 238 U H3 H N N 239 U H5 H N N 240 U H6 H N N 241 # 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 BDG C5 O5 sing N N 40 BDG C5 C4 sing N N 41 BDG C5 C6 sing N N 42 BDG C5 H5 sing N N 43 BDG O5 C1 sing N N 44 BDG C1 O1 sing N N 45 BDG C1 C2 sing N N 46 BDG C1 H1 sing N N 47 BDG O1 HO1 sing N N 48 BDG C2 N2 sing N N 49 BDG C2 C3 sing N N 50 BDG C2 H2 sing N N 51 BDG N2 HN21 sing N N 52 BDG N2 HN22 sing N N 53 BDG C3 O3 sing N N 54 BDG C3 C4 sing N N 55 BDG C3 H3 sing N N 56 BDG O3 HO3 sing N N 57 BDG C4 O4 sing N N 58 BDG C4 H4 sing N N 59 BDG O4 HO4 sing N N 60 BDG C6 N6 sing N N 61 BDG C6 H61 sing N N 62 BDG C6 H62 sing N N 63 BDG N6 HN61 sing N N 64 BDG N6 HN62 sing N N 65 C OP3 P sing N N 66 C OP3 HOP3 sing N N 67 C P OP1 doub N N 68 C P OP2 sing N N 69 C P "O5'" sing N N 70 C OP2 HOP2 sing N N 71 C "O5'" "C5'" sing N N 72 C "C5'" "C4'" sing N N 73 C "C5'" "H5'" sing N N 74 C "C5'" "H5''" sing N N 75 C "C4'" "O4'" sing N N 76 C "C4'" "C3'" sing N N 77 C "C4'" "H4'" sing N N 78 C "O4'" "C1'" sing N N 79 C "C3'" "O3'" sing N N 80 C "C3'" "C2'" sing N N 81 C "C3'" "H3'" sing N N 82 C "O3'" "HO3'" sing N N 83 C "C2'" "O2'" sing N N 84 C "C2'" "C1'" sing N N 85 C "C2'" "H2'" sing N N 86 C "O2'" "HO2'" sing N N 87 C "C1'" N1 sing N N 88 C "C1'" "H1'" sing N N 89 C N1 C2 sing N N 90 C N1 C6 sing N N 91 C C2 O2 doub N N 92 C C2 N3 sing N N 93 C N3 C4 doub N N 94 C C4 N4 sing N N 95 C C4 C5 sing N N 96 C N4 H41 sing N N 97 C N4 H42 sing N N 98 C C5 C6 doub N N 99 C C5 H5 sing N N 100 C C6 H6 sing N N 101 CYY C1 C2 sing N N 102 CYY C1 C6 sing N N 103 CYY C1 N1 sing N N 104 CYY C1 H1 sing N N 105 CYY C2 C3 sing N N 106 CYY C2 H21 sing N N 107 CYY C2 H22 sing N N 108 CYY C3 C4 sing N N 109 CYY C3 N3 sing N N 110 CYY C3 H3 sing N N 111 CYY C4 C5 sing N N 112 CYY C4 O4 sing N N 113 CYY C4 H4 sing N N 114 CYY C5 C6 sing N N 115 CYY C5 O5 sing N N 116 CYY C5 H5 sing N N 117 CYY C6 O6 sing N N 118 CYY C6 H6 sing N N 119 CYY N1 HN11 sing N N 120 CYY N1 HN12 sing N N 121 CYY N3 HN31 sing N N 122 CYY N3 HN32 sing N N 123 CYY O4 HO4 sing N N 124 CYY O5 HO5 sing N N 125 CYY O6 HO6 sing N N 126 G OP3 P sing N N 127 G OP3 HOP3 sing N N 128 G P OP1 doub N N 129 G P OP2 sing N N 130 G P "O5'" sing N N 131 G OP2 HOP2 sing N N 132 G "O5'" "C5'" sing N N 133 G "C5'" "C4'" sing N N 134 G "C5'" "H5'" sing N N 135 G "C5'" "H5''" sing N N 136 G "C4'" "O4'" sing N N 137 G "C4'" "C3'" sing N N 138 G "C4'" "H4'" sing N N 139 G "O4'" "C1'" sing N N 140 G "C3'" "O3'" sing N N 141 G "C3'" "C2'" sing N N 142 G "C3'" "H3'" sing N N 143 G "O3'" "HO3'" sing N N 144 G "C2'" "O2'" sing N N 145 G "C2'" "C1'" sing N N 146 G "C2'" "H2'" sing N N 147 G "O2'" "HO2'" sing N N 148 G "C1'" N9 sing N N 149 G "C1'" "H1'" sing N N 150 G N9 C8 sing Y N 151 G N9 C4 sing Y N 152 G C8 N7 doub Y N 153 G C8 H8 sing N N 154 G N7 C5 sing Y N 155 G C5 C6 sing N N 156 G C5 C4 doub Y N 157 G C6 O6 doub N N 158 G C6 N1 sing N N 159 G N1 C2 sing N N 160 G N1 H1 sing N N 161 G C2 N2 sing N N 162 G C2 N3 doub N N 163 G N2 H21 sing N N 164 G N2 H22 sing N N 165 G N3 C4 sing N N 166 IDG C5 O5 sing N N 167 IDG C5 C4 sing N N 168 IDG C5 C6 sing N N 169 IDG C5 H5 sing N N 170 IDG O5 C1 sing N N 171 IDG C1 O1 sing N N 172 IDG C1 C2 sing N N 173 IDG C1 H1 sing N N 174 IDG O1 HO1 sing N N 175 IDG C2 N2 sing N N 176 IDG C2 C3 sing N N 177 IDG C2 H2 sing N N 178 IDG N2 HN21 sing N N 179 IDG N2 HN22 sing N N 180 IDG C3 O3 sing N N 181 IDG C3 C4 sing N N 182 IDG C3 H3 sing N N 183 IDG O3 HO3 sing N N 184 IDG C4 O4 sing N N 185 IDG C4 H4 sing N N 186 IDG O4 HO4 sing N N 187 IDG C6 N6 sing N N 188 IDG C6 H61 sing N N 189 IDG C6 H62 sing N N 190 IDG N6 HN61 sing N N 191 IDG N6 HN62 sing N N 192 RIB O5 C5 sing N N 193 RIB O5 HO5 sing N N 194 RIB C5 C4 sing N N 195 RIB C5 H51 sing N N 196 RIB C5 H52 sing N N 197 RIB C4 O4 sing N N 198 RIB C4 C3 sing N N 199 RIB C4 H4 sing N N 200 RIB O4 C1 sing N N 201 RIB C3 O3 sing N N 202 RIB C3 C2 sing N N 203 RIB C3 H3 sing N N 204 RIB O3 HO3 sing N N 205 RIB C2 O2 sing N N 206 RIB C2 C1 sing N N 207 RIB C2 H2 sing N N 208 RIB O2 HO2 sing N N 209 RIB C1 O1 sing N N 210 RIB C1 H1 sing N N 211 RIB O1 HO1 sing N N 212 U OP3 P sing N N 213 U OP3 HOP3 sing N N 214 U P OP1 doub N N 215 U P OP2 sing N N 216 U P "O5'" sing N N 217 U OP2 HOP2 sing N N 218 U "O5'" "C5'" sing N N 219 U "C5'" "C4'" sing N N 220 U "C5'" "H5'" sing N N 221 U "C5'" "H5''" sing N N 222 U "C4'" "O4'" sing N N 223 U "C4'" "C3'" sing N N 224 U "C4'" "H4'" sing N N 225 U "O4'" "C1'" sing N N 226 U "C3'" "O3'" sing N N 227 U "C3'" "C2'" sing N N 228 U "C3'" "H3'" sing N N 229 U "O3'" "HO3'" sing N N 230 U "C2'" "O2'" sing N N 231 U "C2'" "C1'" sing N N 232 U "C2'" "H2'" sing N N 233 U "O2'" "HO2'" sing N N 234 U "C1'" N1 sing N N 235 U "C1'" "H1'" sing N N 236 U N1 C2 sing N N 237 U N1 C6 sing N N 238 U C2 O2 doub N N 239 U C2 N3 sing N N 240 U N3 C4 sing N N 241 U N3 H3 sing N N 242 U C4 O4 doub N N 243 U C4 C5 sing N N 244 U C5 C6 doub N N 245 U C5 H5 sing N N 246 U C6 H6 sing N N 247 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1QD3 'double helix' 1QD3 'a-form double helix' 1QD3 'hairpin loop' 1QD3 'bulge loop' # 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 29 1_555 -0.109 -0.128 -0.011 -0.294 0.229 -1.576 1 A_G17:C45_A A 17 ? A 45 ? 19 1 1 A C 2 1_555 A G 28 1_555 0.123 -0.098 -0.029 2.754 -3.057 0.079 2 A_C18:G44_A A 18 ? A 44 ? 19 1 1 A C 3 1_555 A G 27 1_555 0.220 -0.160 -0.013 -0.094 -0.317 -2.684 3 A_C19:G43_A A 19 ? A 43 ? 19 1 1 A A 4 1_555 A U 26 1_555 -0.083 -0.111 -0.051 -0.780 0.509 -3.203 4 A_A20:U42_A A 20 ? A 42 ? 20 1 1 A G 5 1_555 A C 25 1_555 -0.158 -0.152 -0.026 -0.808 0.621 1.334 5 A_G21:C41_A A 21 ? A 41 ? 19 1 1 A A 6 1_555 A U 24 1_555 -0.426 -0.489 -0.043 21.790 4.485 -5.536 6 A_A22:U40_A A 22 ? A 40 ? 20 1 1 A G 10 1_555 A C 23 1_555 -0.112 -0.129 -0.062 -0.945 -0.635 0.034 7 A_G26:C39_A A 26 ? A 39 ? 19 1 1 A A 11 1_555 A U 22 1_555 -0.037 -0.172 -0.029 -2.054 -0.586 7.271 8 A_A27:U38_A A 27 ? A 38 ? 20 1 1 A G 12 1_555 A C 21 1_555 -0.148 -0.143 -0.077 -0.238 0.693 -2.807 9 A_G28:C37_A A 28 ? A 37 ? 19 1 1 A C 13 1_555 A G 20 1_555 0.154 -0.130 0.054 -0.384 -1.625 -1.036 10 A_C29:G36_A A 29 ? A 36 ? 19 1 1 A C 14 1_555 A G 18 1_555 3.457 -1.227 2.487 -23.659 5.659 40.261 11 A_C30:G34_A A 30 ? A 34 ? ? ? # 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 29 1_555 A C 2 1_555 A G 28 1_555 -1.543 -1.669 3.268 1.841 7.024 14.478 -10.213 6.601 2.030 25.853 -6.777 16.188 1 AA_G17C18:G44C45_AA A 17 ? A 45 ? A 18 ? A 44 ? 1 A C 2 1_555 A G 28 1_555 A C 3 1_555 A G 27 1_555 0.944 -2.543 2.759 9.261 28.603 27.459 -5.513 -0.767 0.342 46.171 -14.948 40.503 2 AA_C18C19:G43G44_AA A 18 ? A 44 ? A 19 ? A 43 ? 1 A C 3 1_555 A G 27 1_555 A A 4 1_555 A U 26 1_555 1.250 -1.626 3.558 -1.191 -15.902 34.962 -0.101 -2.081 3.872 -24.929 1.867 38.323 3 AA_C19A20:U42G43_AA A 19 ? A 43 ? A 20 ? A 42 ? 1 A A 4 1_555 A U 26 1_555 A G 5 1_555 A C 25 1_555 0.417 -1.904 2.889 0.769 16.071 31.696 -4.904 -0.600 1.759 27.332 -1.308 35.452 4 AA_A20G21:C41U42_AA A 20 ? A 42 ? A 21 ? A 41 ? 1 A G 5 1_555 A C 25 1_555 A A 6 1_555 A U 24 1_555 -0.548 -0.649 2.720 0.472 11.604 13.473 -7.303 1.987 1.629 40.891 -1.664 17.770 5 AA_G21A22:U40C41_AA A 21 ? A 41 ? A 22 ? A 40 ? 1 A A 6 1_555 A U 24 1_555 A G 10 1_555 A C 23 1_555 -0.758 -2.095 3.117 -8.271 9.237 58.271 -2.543 0.378 2.859 9.370 8.390 59.462 6 AA_A22G26:C39U40_AA A 22 ? A 40 ? A 26 ? A 39 ? 1 A G 10 1_555 A C 23 1_555 A A 11 1_555 A U 22 1_555 1.271 -1.467 2.815 1.660 7.951 44.503 -2.498 -1.530 2.573 10.395 -2.170 45.201 7 AA_G26A27:U38C39_AA A 26 ? A 39 ? A 27 ? A 38 ? 1 A A 11 1_555 A U 22 1_555 A G 12 1_555 A C 21 1_555 -0.350 -1.694 3.002 1.256 6.300 24.160 -5.511 1.127 2.466 14.721 -2.936 24.987 8 AA_A27G28:C37U38_AA A 27 ? A 38 ? A 28 ? A 37 ? 1 A G 12 1_555 A C 21 1_555 A C 13 1_555 A G 20 1_555 -0.360 -2.676 3.130 -1.656 -1.493 27.109 -5.322 0.358 3.286 -3.179 3.525 27.199 9 AA_G28C29:G36C37_AA A 28 ? A 37 ? A 29 ? A 36 ? 1 A C 13 1_555 A G 20 1_555 A C 14 1_555 A G 18 1_555 2.382 0.232 3.881 -10.179 13.087 52.339 -0.641 -3.286 3.364 14.431 11.224 54.725 10 AA_C29C30:G34G36_AA A 29 ? A 36 ? A 30 ? A 34 ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 RIB 1 n 2 IDG 2 n # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 DRX600 Bruker 600 ? 2 DMX750 Bruker 750 ? # _atom_sites.entry_id 1QD3 _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_