data_2JUK # _entry.id 2JUK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2JUK pdb_00002juk 10.2210/pdb2juk/pdb RCSB RCSB100308 ? ? WWPDB D_1000100308 ? ? # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2JUK _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-08-30 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _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 'Staple, D.W.' 1 'Venditti, V.' 2 'Niccolai, N.' 3 'Elson-Schwab, L.' 4 'Tor, Y.' 5 'Butcher, S.E.' 6 # _citation.id primary _citation.title 'Guanidinoneomycin B Recognition of an HIV-1 RNA Helix.' _citation.journal_abbrev Chembiochem _citation.journal_volume 9 _citation.page_first 93 _citation.page_last 102 _citation.year 2008 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1439-4227 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18058789 _citation.pdbx_database_id_DOI 10.1002/cbic.200700251 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Staple, D.W.' 1 ? primary 'Venditti, V.' 2 ? primary 'Niccolai, N.' 3 ? primary 'Elson-Schwab, L.' 4 ? primary 'Tor, Y.' 5 ? primary 'Butcher, S.E.' 6 ? # _cell.entry_id 2JUK _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 2JUK _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 'HIV-1 frameshift site RNA' 7071.299 1 ? ? ? ? 2 non-polymer syn ;(1S,2R,3S,4R,6S)-4,6-bis{[amino(iminio)methyl]amino}-2-{[3-O-(2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranosyl)-beta-D-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranoside ; 872.931 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 GGCCUUCCCACAAGGGAAGGCC _entity_poly.pdbx_seq_one_letter_code_can GGCCUUCCCACAAGGGAAGGCC _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 C n 1 5 U n 1 6 U n 1 7 C n 1 8 C n 1 9 C n 1 10 A n 1 11 C n 1 12 A n 1 13 A n 1 14 G n 1 15 G n 1 16 G n 1 17 A n 1 18 A n 1 19 G n 1 20 G n 1 21 C n 1 22 C n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2JUK _struct_ref.pdbx_db_accession 2JUK _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2JUK _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 22 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2JUK _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 22 _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 22 # 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 G0B non-polymer . ;(1S,2R,3S,4R,6S)-4,6-bis{[amino(iminio)methyl]amino}-2-{[3-O-(2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranosyl)-beta-D-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranoside ; ? 'C29 H64 N18 O13 6' 872.931 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H NOESY' 1 2 1 '2D 1H-1H TOCSY' 1 3 1 '2D HMBC' 1 4 1 '2D 1H-13C HSQC' 1 5 1 '2D 1H-13C HSQC' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 50 _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 303 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '1mM mM HIV-1 frameshift site RNA, 0.5mM mM [U,G,C,A] 100% 15N, 100% 13C HIV-1 frameshift site RNA, 100% D2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '100% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 750 Bruker DMX 1 'Bruker DMX' 600 Bruker DMX 2 'Bruker DMX' 900 Varian INOVA 3 'Varian INOVA' 800 Varian INOVA 4 'Varian INOVA' # _pdbx_nmr_refine.entry_id 2JUK _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2JUK _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2JUK _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Case, D.A. et al.' refinement Amber ? 1 'Brunger, A.T. et al.' 'structure solution' CNS ? 2 'Koradi, R. et al.' 'structure visualization' MOLMOL ? 3 'Goddard, T.D. et al.' 'chemical shift assignment' Sparky ? 4 'Schwieters, C.D. et al.' 'structure solution' 'X-PLOR NIH' ? 5 'Bruker Biospin' collection XwinNMR ? 6 'Delaglio, F. et al.' collection NMRPipe ? 7 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2JUK _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2JUK _struct.title 'guanidino neomycin B recognition of an HIV-1 RNA helix' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2JUK _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HIV-1, RNA-ligand interactions, guanidinoglycosides, 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 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 1 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 1 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 1 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 2 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 2 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 2 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 3 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 3 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 3 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 19 N1 ? ? A C 4 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 19 O6 ? ? A C 4 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 19 N2 ? ? A C 4 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 18 N1 ? ? A U 5 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 18 N6 ? ? A U 5 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 17 N1 ? ? A U 6 A A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 17 N6 ? ? A U 6 A A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 7 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 7 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 7 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 8 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 8 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 8 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 14 N1 ? ? A C 9 A G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 14 O6 ? ? A C 9 A G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 14 N2 ? ? A C 9 A G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 10 N3 ? ? ? 1_555 A A 13 N6 ? ? A A 10 A A 13 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id G0B _struct_site.pdbx_auth_seq_id 23 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 10 _struct_site.details 'BINDING SITE FOR RESIDUE G0B A 23' # 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 10 C A 3 ? C A 3 . ? 1_555 ? 2 AC1 10 C A 4 ? C A 4 . ? 1_555 ? 3 AC1 10 U A 5 ? U A 5 . ? 1_555 ? 4 AC1 10 U A 6 ? U A 6 . ? 1_555 ? 5 AC1 10 C A 7 ? C A 7 . ? 1_555 ? 6 AC1 10 C A 8 ? C A 8 . ? 1_555 ? 7 AC1 10 C A 9 ? C A 9 . ? 1_555 ? 8 AC1 10 A A 10 ? A A 10 . ? 1_555 ? 9 AC1 10 C A 11 ? C A 11 . ? 1_555 ? 10 AC1 10 A A 17 ? A A 17 . ? 1_555 ? # _atom_sites.entry_id 2JUK _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 C 4 4 4 C C A . n A 1 5 U 5 5 5 U U A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 A 12 12 12 A A 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 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 G 19 19 19 G G A . n A 1 20 G 20 20 20 G G A . n A 1 21 C 21 21 21 C C A . n A 1 22 C 22 22 22 C C A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id G0B _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 23 _pdbx_nonpoly_scheme.auth_seq_num 23 _pdbx_nonpoly_scheme.pdb_mon_id G0B _pdbx_nonpoly_scheme.auth_mon_id G0B _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2007-11-20 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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 3 'Structure model' database_2 2 3 'Structure model' pdbx_nmr_software 3 3 'Structure model' pdbx_struct_assembly 4 3 'Structure model' pdbx_struct_oper_list 5 3 'Structure model' struct_site # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_nmr_software.name' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id 'HIV-1 frameshift site RNA' 1 mM ? 1 'HIV-1 frameshift site RNA' 0.5 mM '[U,G,C,A] 100% 15N, 100% 13C' 2 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 13 _pdbx_validate_close_contact.auth_atom_id_1 "HO2'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 C _pdbx_validate_close_contact.auth_seq_id_1 11 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OP2 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 A _pdbx_validate_close_contact.auth_seq_id_2 12 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.57 # 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 C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 112.80 108.50 4.30 0.70 N 2 2 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 113.16 108.50 4.66 0.70 N 3 2 "O4'" A A 13 ? ? "C1'" A A 13 ? ? N9 A A 13 ? ? 112.82 108.50 4.32 0.70 N 4 2 "O4'" A G 14 ? ? "C1'" A G 14 ? ? N9 A G 14 ? ? 112.78 108.50 4.28 0.70 N 5 3 "C5'" A A 12 ? ? "C4'" A A 12 ? ? "C3'" A A 12 ? ? 106.59 115.20 -8.61 1.40 N 6 4 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 113.04 108.50 4.54 0.70 N 7 15 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 112.74 108.50 4.24 0.70 N 8 16 "O4'" A A 12 ? ? "C1'" A A 12 ? ? N9 A A 12 ? ? 112.73 108.50 4.23 0.70 N 9 16 "O4'" A A 13 ? ? "C1'" A A 13 ? ? N9 A A 13 ? ? 113.03 108.50 4.53 0.70 N 10 17 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 114.05 108.50 5.55 0.70 N 11 19 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 112.74 108.50 4.24 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2JUK 'double helix' 2JUK 'a-form double helix' 2JUK 'hairpin loop' 2JUK '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 22 1_555 -0.072 -0.045 -0.634 -19.998 -7.300 -1.727 1 A_G1:C22_A A 1 ? A 22 ? 19 1 1 A G 2 1_555 A C 21 1_555 -0.441 -0.112 0.196 13.838 4.599 -1.363 2 A_G2:C21_A A 2 ? A 21 ? 19 1 1 A C 3 1_555 A G 20 1_555 0.143 -0.046 -1.006 33.293 -12.032 -1.639 3 A_C3:G20_A A 3 ? A 20 ? 19 1 1 A C 4 1_555 A G 19 1_555 0.295 -0.281 -1.189 20.782 -16.964 2.585 4 A_C4:G19_A A 4 ? A 19 ? 19 1 1 A U 5 1_555 A A 18 1_555 0.617 -0.232 -0.739 -41.610 -15.721 -13.033 5 A_U5:A18_A A 5 ? A 18 ? 20 1 1 A U 6 1_555 A A 17 1_555 -0.061 -0.018 0.324 -24.930 6.605 3.784 6 A_U6:A17_A A 6 ? A 17 ? 20 1 1 A C 7 1_555 A G 16 1_555 0.443 -0.160 -0.554 15.562 0.492 -2.718 7 A_C7:G16_A A 7 ? A 16 ? 19 1 1 A C 8 1_555 A G 15 1_555 0.069 -0.171 -1.129 26.207 -3.289 -5.053 8 A_C8:G15_A A 8 ? A 15 ? 19 1 1 A C 9 1_555 A G 14 1_555 -0.033 -0.250 -0.561 -2.682 20.353 -7.648 9 A_C9:G14_A A 9 ? A 14 ? 19 1 1 A A 10 1_555 A A 13 1_555 5.775 -4.399 1.537 17.366 24.643 7.497 10 A_A10:A13_A A 10 ? A 13 ? ? ? # 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 22 1_555 A G 2 1_555 A C 21 1_555 0.004 -0.925 2.641 -5.584 1.326 21.758 -2.762 -1.654 2.501 3.436 14.471 22.494 1 AA_G1G2:C21C22_AA A 1 ? A 22 ? A 2 ? A 21 ? 1 A G 2 1_555 A C 21 1_555 A C 3 1_555 A G 20 1_555 0.208 -1.253 3.036 6.669 7.354 28.486 -3.746 0.811 2.619 14.403 -13.061 30.132 2 AA_G2C3:G20C21_AA A 2 ? A 21 ? A 3 ? A 20 ? 1 A C 3 1_555 A G 20 1_555 A C 4 1_555 A G 19 1_555 0.631 -1.742 3.871 2.446 14.043 32.132 -5.179 -0.648 2.919 23.954 -4.172 35.076 3 AA_C3C4:G19G20_AA A 3 ? A 20 ? A 4 ? A 19 ? 1 A C 4 1_555 A G 19 1_555 A U 5 1_555 A A 18 1_555 -0.374 -2.382 5.230 1.924 32.499 32.994 -6.797 0.700 2.149 45.720 -2.707 46.031 4 AA_C4U5:A18G19_AA A 4 ? A 19 ? A 5 ? A 18 ? 1 A U 5 1_555 A A 18 1_555 A U 6 1_555 A A 17 1_555 0.533 -0.948 3.236 -8.497 4.255 25.826 -2.981 -3.090 2.737 9.136 18.242 27.491 5 AA_U5U6:A17A18_AA A 5 ? A 18 ? A 6 ? A 17 ? 1 A U 6 1_555 A A 17 1_555 A C 7 1_555 A G 16 1_555 -0.238 -1.117 2.565 4.701 -1.531 25.104 -2.180 1.589 2.541 -3.479 -10.682 25.579 6 AA_U6C7:G16A17_AA A 6 ? A 17 ? A 7 ? A 16 ? 1 A C 7 1_555 A G 16 1_555 A C 8 1_555 A G 15 1_555 -0.065 -1.481 3.361 1.496 9.421 25.085 -5.501 0.507 2.633 20.757 -3.297 26.811 7 AA_C7C8:G15G16_AA A 7 ? A 16 ? A 8 ? A 15 ? 1 A C 8 1_555 A G 15 1_555 A C 9 1_555 A G 14 1_555 -1.542 -1.847 4.566 -7.566 34.350 32.819 -5.690 1.154 2.133 47.160 10.387 47.750 8 AA_C8C9:G14G15_AA A 8 ? A 15 ? A 9 ? A 14 ? 1 A C 9 1_555 A G 14 1_555 A A 10 1_555 A A 13 1_555 -0.173 -0.441 2.743 -7.350 20.626 57.012 -1.261 -0.123 2.471 20.784 7.406 60.742 9 AA_C9A10:A13G14_AA A 9 ? A 14 ? A 10 ? A 13 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name ;(1S,2R,3S,4R,6S)-4,6-bis{[amino(iminio)methyl]amino}-2-{[3-O-(2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranosyl)-beta-D-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranoside ; _pdbx_entity_nonpoly.comp_id G0B #