data_1P5N # _entry.id 1P5N # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1P5N pdb_00001p5n 10.2210/pdb1p5n/pdb RCSB RCSB019037 ? ? WWPDB D_1000019037 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1P5N _pdbx_database_status.recvd_initial_deposition_date 2003-04-27 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Lukavsky, P.J.' 1 'Kim, I.' 2 'Otto, G.A.' 3 'Puglisi, J.D.' 4 # _citation.id primary _citation.title 'Structure of HCV IRES domain II determined by NMR.' _citation.journal_abbrev Nat.Struct.Biol. _citation.journal_volume 10 _citation.page_first 1033 _citation.page_last 1038 _citation.year 2003 _citation.journal_id_ASTM NSBIEW _citation.country US _citation.journal_id_ISSN 1072-8368 _citation.journal_id_CSD 2024 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14578934 _citation.pdbx_database_id_DOI 10.1038/nsb1004 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lukavsky, P.J.' 1 ? primary 'Kim, I.' 2 ? primary 'Otto, G.A.' 3 ? primary 'Puglisi, J.D.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 34-MER _entity.formula_weight 10970.565 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'HCV IRES domain IIa (residues 69-98)' _entity.details ? # _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 GGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGCC _entity_poly.pdbx_seq_one_letter_code_can GGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 A n 1 5 G n 1 6 A n 1 7 A n 1 8 A n 1 9 G n 1 10 C n 1 11 G n 1 12 U n 1 13 C n 1 14 U n 1 15 A n 1 16 G n 1 17 C n 1 18 C n 1 19 A n 1 20 U n 1 21 G n 1 22 G n 1 23 C n 1 24 G n 1 25 U n 1 26 U n 1 27 A n 1 28 G n 1 29 U n 1 30 A n 1 31 U n 1 32 G 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 ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Synthesized by in vitro transcription from linearized plasmid DNA using T7 RNA polymerase' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1P5N _struct_ref.pdbx_db_accession 1P5N _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 1P5N _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 1P5N _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 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D S-NOESY' 2 2 2 '2D NOESY' 3 2 2 DQF-COSY 4 2 2 '2D HP-COSY' 5 4 2 3D_13C-separated_NOESY 6 4 2 '3D HCP' 7 3 2 '3D HMQC TOCSY' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 288 ambient 6.40 '10mM posphate buffer' ? K 2 298 ambient 6.40 '10mM posphate buffer' ? K 3 303 ambient 6.40 '10mM posphate buffer' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer' '96% D2O, 4% H2O' 2 '1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer' '100% D2O' 3 ;1-2mM HCV IRES domain IIb RNA U-15N,13C 10mM phosphate buffer ; '96% D2O, 4% H2O' 4 ;1-2mM HCV IRES domain IIb RNA U-15N,13C 10mM phosphate buffer ; '100% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Varian INOVA 500 2 ? Varian INOVA 800 # _pdbx_nmr_refine.entry_id 1P5N _pdbx_nmr_refine.method 'see reference above' _pdbx_nmr_refine.details 'see reference above' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1P5N _pdbx_nmr_details.text ;The structure was solved using triple resonance, multidimensional NMR spectroscopy and TROSY-type experiments to measure residual dipolar couplings ; # _pdbx_nmr_ensemble.entry_id 1P5N _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'lowest restraint violation and total energy' _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_representative.entry_id 1P5N _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal VNMR 6.1C processing Varian 1 Sparky 3 'data analysis' 'Goddard, T.D. & Kneller D.G.' 2 X-PLOR 3.1 refinement 'Brunger, A.T.' 3 CNS 1.1 refinement 'Brunger, A.T.' 4 PALES 1 refinement 'Zweckstetter, M. & Bax, A.' 5 # _exptl.entry_id 1P5N _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 # _struct.entry_id 1P5N _struct.title 'Solution Structure of HCV IRES Domain IIb' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1P5N _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RIBONUCLEIC ACID, HEPATITIS C VIRUS, INTERNAL RIBOSOME ENTRY SITE, LOOP E MOTIF, HAIRPIN LOOP, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _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 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 C 3 N3 ? ? ? 1_555 A G 32 N1 ? ? A C 3 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 32 O6 ? ? A C 3 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 32 N2 ? ? A C 3 A G 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 N2 ? ? ? 1_555 A A 30 N7 ? ? A G 5 A A 30 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog13 hydrog ? ? A G 5 N3 ? ? ? 1_555 A A 30 N6 ? ? A G 5 A A 30 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog14 hydrog ? ? A G 5 N2 ? ? ? 1_555 A U 31 O4 ? ? A G 5 A U 31 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog15 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 29 O2 ? ? A A 6 A U 29 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog16 hydrog ? ? A A 6 N7 ? ? ? 1_555 A U 29 N3 ? ? A A 6 A U 29 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog17 hydrog ? ? A A 7 N6 ? ? ? 1_555 A A 27 N7 ? ? A A 7 A A 27 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog18 hydrog ? ? A A 7 N7 ? ? ? 1_555 A A 27 N6 ? ? A A 7 A A 27 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog19 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 26 O2 ? ? A A 8 A U 26 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 A U 25 O2 ? ? A G 9 A U 25 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A G 9 O6 ? ? ? 1_555 A U 25 N3 ? ? A G 9 A U 25 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 24 N1 ? ? A C 10 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 24 O6 ? ? A C 10 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 24 N2 ? ? A C 10 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 11 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 11 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 11 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 12 N3 ? ? ? 1_555 A G 22 O6 ? ? A U 12 A G 22 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog29 hydrog ? ? A U 12 O2 ? ? ? 1_555 A G 22 N1 ? ? A U 12 A G 22 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog30 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 13 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 13 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 13 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 14 O2 ? ? ? 1_555 A G 21 N1 ? ? A U 14 A G 21 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog34 hydrog ? ? A A 27 N1 ? ? ? 1_555 A G 28 N2 ? ? A A 27 A G 28 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog35 hydrog ? ? A G 28 N2 ? ? ? 1_555 A U 29 O4 ? ? A G 28 A U 29 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1P5N _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1P5N _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 GUA A . n A 1 2 G 2 2 2 G GUA A . n A 1 3 C 3 3 3 C CYT A . n A 1 4 A 4 4 4 A ADE A . n A 1 5 G 5 5 5 G GUA A . n A 1 6 A 6 6 6 A ADE A . n A 1 7 A 7 7 7 A ADE A . n A 1 8 A 8 8 8 A ADE A . n A 1 9 G 9 9 9 G GUA A . n A 1 10 C 10 10 10 C CYT A . n A 1 11 G 11 11 11 G GUA A . n A 1 12 U 12 12 12 U URI A . n A 1 13 C 13 13 13 C CYT A . n A 1 14 U 14 14 14 U URI A . n A 1 15 A 15 15 15 A ADE A . n A 1 16 G 16 16 16 G GUA A . n A 1 17 C 17 17 17 C CYT A . n A 1 18 C 18 18 18 C CYT A . n A 1 19 A 19 19 19 A ADE A . n A 1 20 U 20 20 20 U URI A . n A 1 21 G 21 21 21 G GUA A . n A 1 22 G 22 22 22 G GUA A . n A 1 23 C 23 23 23 C CYT A . n A 1 24 G 24 24 24 G GUA A . n A 1 25 U 25 25 25 U URI A . n A 1 26 U 26 26 26 U URI A . n A 1 27 A 27 27 27 A ADE A . n A 1 28 G 28 28 28 G GUA A . n A 1 29 U 29 29 29 U URI A . n A 1 30 A 30 30 30 A ADE A . n A 1 31 U 31 31 31 U URI A . n A 1 32 G 32 32 32 G GUA A . n A 1 33 C 33 33 33 C CYT A . n A 1 34 C 34 34 34 C CYT A . n # _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 # _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 2003-11-04 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # 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' '_pdbx_nmr_software.name' # 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 O6 A G 5 ? ? "HO2'" A G 28 ? ? 1.59 2 3 "O2'" A U 20 ? ? H8 A G 21 ? ? 1.57 3 4 O6 A G 5 ? ? "HO2'" A G 28 ? ? 1.60 4 8 O6 A G 5 ? ? "HO2'" A G 28 ? ? 1.59 5 9 O6 A G 5 ? ? "HO2'" A G 28 ? ? 1.57 6 10 H61 A A 8 ? ? "O2'" A U 26 ? ? 1.60 7 11 O6 A G 5 ? ? "HO2'" A G 28 ? ? 1.58 8 13 "O2'" A U 20 ? ? H8 A G 21 ? ? 1.59 9 15 O6 A G 5 ? ? "HO2'" A G 28 ? ? 1.56 10 15 H61 A A 8 ? ? "O2'" A U 26 ? ? 1.58 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1P5N 'double helix' 1P5N 'a-form double helix' 1P5N 'hairpin loop' 1P5N 'bulge loop' 1P5N 'mismatched base pair' 1P5N 'quadruple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 34 1_555 0.107 -0.351 -0.608 28.061 -25.618 18.413 1 A_G1:C34_A A 1 ? A 34 ? 19 1 1 A G 2 1_555 A C 33 1_555 0.239 -0.110 -0.528 2.527 -22.536 9.576 2 A_G2:C33_A A 2 ? A 33 ? 19 1 1 A C 3 1_555 A G 32 1_555 -0.038 -0.191 -1.034 19.075 -28.690 4.161 3 A_C3:G32_A A 3 ? A 32 ? 19 1 1 A A 4 1_555 A U 31 1_555 0.392 0.163 -1.420 -37.722 -0.430 -6.450 4 A_A4:U31_A A 4 ? A 31 ? 20 1 1 A G 5 1_555 A A 30 1_555 6.503 -3.229 -0.911 -0.429 9.448 -5.701 5 A_G5:A30_A A 5 ? A 30 ? 11 9 1 A A 6 1_555 A U 29 1_555 -4.043 -1.469 -0.941 0.468 -16.713 -109.859 6 A_A6:U29_A A 6 ? A 29 ? 24 4 1 A A 7 1_555 A A 27 1_555 -5.569 4.838 0.681 -19.135 -10.294 -177.190 7 A_A7:A27_A A 7 ? A 27 ? 2 8 1 A A 8 1_555 A U 26 1_555 -7.110 -4.101 -0.084 18.339 -18.698 11.387 8 A_A8:U26_A A 8 ? A 26 ? ? 5 1 A G 9 1_555 A U 25 1_555 -2.281 -0.389 -0.140 10.412 -32.654 9.447 9 A_G9:U25_A A 9 ? A 25 ? 28 ? 1 A C 10 1_555 A G 24 1_555 -0.117 -0.119 -0.485 13.838 -32.665 6.623 10 A_C10:G24_A A 10 ? A 24 ? 19 1 1 A G 11 1_555 A C 23 1_555 0.258 -0.292 -0.130 -3.816 -21.733 -2.802 11 A_G11:C23_A A 11 ? A 23 ? 19 1 1 A U 12 1_555 A G 22 1_555 1.472 -0.434 -0.471 4.348 -20.345 -8.860 12 A_U12:G22_A A 12 ? A 22 ? 28 ? 1 A C 13 1_555 A G 21 1_555 -0.417 -0.094 -0.102 2.211 0.466 -2.538 13 A_C13:G21_A A 13 ? A 21 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 34 1_555 A G 2 1_555 A C 33 1_555 -0.382 -0.545 3.858 -1.980 24.374 27.802 -4.621 0.299 2.599 41.913 3.405 36.867 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 C 3 1_555 A G 32 1_555 -0.218 -0.717 2.641 3.704 1.771 33.311 -1.474 0.863 2.562 3.075 -6.431 33.556 2 AA_G2C3:G32C33_AA A 2 ? A 33 ? A 3 ? A 32 ? 1 A C 3 1_555 A G 32 1_555 A A 4 1_555 A U 31 1_555 0.122 -2.111 5.132 -1.048 24.951 29.320 -7.452 -0.364 2.609 41.150 1.728 38.336 3 AA_C3A4:U31G32_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 A 30 1_555 -0.369 -0.169 2.274 -2.662 -3.220 61.334 -0.060 0.274 2.292 -3.153 2.606 61.463 4 AA_A4G5:A30U31_AA A 4 ? A 31 ? A 5 ? A 30 ? 1 A G 5 1_555 A A 30 1_555 A A 6 1_555 A U 29 1_555 -4.654 -1.344 3.251 0.183 13.267 -5.595 -10.016 -18.361 2.563 -67.232 0.927 -14.395 5 AA_G5A6:U29A30_AA A 5 ? A 30 ? A 6 ? A 29 ? 1 A A 6 1_555 A U 29 1_555 A A 7 1_555 A A 27 1_555 1.659 -1.190 2.702 -5.479 -8.991 86.751 -0.700 -1.301 2.704 -6.525 3.977 87.261 6 AA_A6A7:A27U29_AA A 6 ? A 29 ? A 7 ? A 27 ? 1 A A 7 1_555 A A 27 1_555 A A 8 1_555 A U 26 1_555 -0.821 0.981 2.820 0.781 5.623 -59.499 -1.224 -0.791 2.736 -5.652 0.785 -59.744 7 AA_A7A8:U26A27_AA A 7 ? A 27 ? A 8 ? A 26 ? 1 A A 8 1_555 A U 26 1_555 A G 9 1_555 A U 25 1_555 0.041 0.249 3.485 -6.655 7.795 57.579 -0.182 -0.415 3.466 8.022 6.850 58.407 8 AA_A8G9:U25U26_AA A 8 ? A 26 ? A 9 ? A 25 ? 1 A G 9 1_555 A U 25 1_555 A C 10 1_555 A G 24 1_555 -0.219 -0.578 3.181 -0.109 -4.770 44.299 -0.331 0.280 3.224 -6.304 0.143 44.542 9 AA_G9C10:G24U25_AA A 9 ? A 25 ? A 10 ? A 24 ? 1 A C 10 1_555 A G 24 1_555 A G 11 1_555 A C 23 1_555 -0.864 -0.527 3.715 -4.212 18.943 32.917 -3.498 0.727 3.064 30.368 6.752 38.075 10 AA_C10G11:C23G24_AA A 10 ? A 24 ? A 11 ? A 23 ? 1 A G 11 1_555 A C 23 1_555 A U 12 1_555 A G 22 1_555 -0.245 -1.133 2.801 2.240 -1.018 41.561 -1.501 0.548 2.811 -1.433 -3.154 41.630 11 AA_G11U12:G22C23_AA A 11 ? A 23 ? A 12 ? A 22 ? 1 A U 12 1_555 A G 22 1_555 A C 13 1_555 A G 21 1_555 0.879 -1.614 3.450 -0.562 -1.055 28.637 -3.009 -1.910 3.489 -2.132 1.135 28.661 12 AA_U12C13:G21G22_AA A 12 ? A 22 ? A 13 ? A 21 ? #