data_2LP9 # _entry.id 2LP9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 2LP9 pdb_00002lp9 10.2210/pdb2lp9/pdb RCSB RCSB102662 ? ? BMRB 18239 ? ? WWPDB D_1000102662 ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 18239 BMRB unspecified . 2LPA PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LP9 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-02-06 _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.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # _audit_author.name 'Skov, J.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter. ; _citation.journal_abbrev Rna _citation.journal_volume 18 _citation.page_first 992 _citation.page_last 1000 _citation.year 2012 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22393035 _citation.pdbx_database_id_DOI 10.1261/rna.029918.111 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Skov, J.' 1 ? primary 'Gaudin, M.' 2 ? primary 'Podbevsek, P.' 3 ? primary 'Olsthoorn, R.C.' 4 ? primary 'Petersen, M.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3') ; _entity.formula_weight 5122.103 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _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 GAGGACAUAGAUCUUC _entity_poly.pdbx_seq_one_letter_code_can GAGGACAUAGAUCUUC _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 A n 1 3 G n 1 4 G n 1 5 A n 1 6 C n 1 7 A n 1 8 U n 1 9 A n 1 10 G n 1 11 A n 1 12 U n 1 13 C n 1 14 U n 1 15 U n 1 16 C n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2LP9 _struct_ref.pdbx_db_accession 2LP9 _struct_ref.entity_id 1 _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 2LP9 _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 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2LP9 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 16 _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 16 # 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.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 DQF-COSY' 1 4 1 '2D 1H-13C HSQC' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 65 _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents ;2 mM RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 2 mM EDTA, 90% H2O/10% D2O ; _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Varian INOVA' # _pdbx_nmr_refine.entry_id 2LP9 _pdbx_nmr_refine.method 'simulated annealing' _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 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LP9 _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 2LP9 _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 Brunger 'structure solution' X-PLOR 3.851 1 Brunger refinement X-PLOR 3.851 2 # _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 2LP9 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LP9 _struct.title 'Pseudo-triloop from the sub-genomic promoter of Brome Mosaic Virus' _struct.pdbx_model_details 'lowest energy, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LP9 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'pseudo-triloop, RNA replication, 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 _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 16 N3 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N1 ? ? ? 1_555 A U 15 N3 ? ? A A 2 A U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 2 N6 ? ? ? 1_555 A U 15 O4 ? ? A A 2 A U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 A U 14 O2 ? ? A G 3 A U 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog7 hydrog ? ? A G 3 O6 ? ? ? 1_555 A U 14 N3 ? ? A G 3 A U 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 12 N3 ? ? A A 5 A U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 12 O4 ? ? A A 5 A U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 10 N1 ? ? A C 6 A G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 10 O6 ? ? A C 6 A G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 10 N2 ? ? A C 6 A G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 7 N3 ? ? ? 1_555 A A 9 N6 ? ? A A 7 A A 9 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2LP9 _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 A 2 2 2 A A A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 A 7 7 7 A A A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 G 10 10 10 G G A . n A 1 11 A 11 11 11 A A A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 U 14 14 14 U U A . n A 1 15 U 15 15 15 U U A . n A 1 16 C 16 16 16 C C 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 2012-05-16 2 'Structure model' 1 1 2023-06-14 # _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' 'Database references' 2 2 'Structure model' Other # 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 2 'Structure model' database_2 2 2 'Structure model' pdbx_database_status # 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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id ;RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3')-1 ; 2 ? mM ? 1 'sodium phosphate-2' 10 ? mM ? 1 'sodium chloride-3' 50 ? mM ? 1 EDTA-4 2 ? mM ? 1 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2LP9 _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 272 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # 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 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 113.35 108.50 4.85 0.70 N 2 1 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 113.61 108.50 5.11 0.70 N 3 1 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.79 108.50 5.29 0.70 N 4 1 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.74 108.50 5.24 0.70 N 5 1 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.59 108.50 5.09 0.70 N 6 1 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.56 108.50 5.06 0.70 N 7 2 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 113.41 108.50 4.91 0.70 N 8 2 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 115.46 108.50 6.96 0.70 N 9 2 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.43 108.50 4.93 0.70 N 10 2 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.73 108.50 5.23 0.70 N 11 2 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.21 108.50 4.71 0.70 N 12 2 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.46 108.50 4.96 0.70 N 13 3 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 113.15 108.50 4.65 0.70 N 14 3 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 113.14 108.50 4.64 0.70 N 15 3 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.35 108.50 4.85 0.70 N 16 3 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.66 108.50 5.16 0.70 N 17 3 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.65 108.50 5.15 0.70 N 18 3 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.41 108.50 4.91 0.70 N 19 4 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 113.01 108.50 4.51 0.70 N 20 4 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 112.93 108.50 4.43 0.70 N 21 4 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.12 108.50 4.62 0.70 N 22 4 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.73 108.50 5.23 0.70 N 23 4 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.82 108.50 5.32 0.70 N 24 4 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.56 108.50 5.06 0.70 N 25 5 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 112.94 108.50 4.44 0.70 N 26 5 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 113.20 108.50 4.70 0.70 N 27 5 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.22 108.50 4.72 0.70 N 28 5 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.83 108.50 5.33 0.70 N 29 5 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.74 108.50 5.24 0.70 N 30 5 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.38 108.50 4.88 0.70 N 31 6 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 113.54 108.50 5.04 0.70 N 32 6 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 112.81 108.50 4.31 0.70 N 33 6 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 112.85 108.50 4.35 0.70 N 34 6 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.49 108.50 4.99 0.70 N 35 6 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.75 108.50 5.25 0.70 N 36 6 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.52 108.50 5.02 0.70 N 37 7 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 112.76 108.50 4.26 0.70 N 38 7 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 113.03 108.50 4.53 0.70 N 39 7 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 112.99 108.50 4.49 0.70 N 40 7 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.58 108.50 5.08 0.70 N 41 7 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.64 108.50 5.14 0.70 N 42 7 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.53 108.50 5.03 0.70 N 43 8 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 112.77 108.50 4.27 0.70 N 44 8 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 113.09 108.50 4.59 0.70 N 45 8 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.19 108.50 4.69 0.70 N 46 8 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.71 108.50 5.21 0.70 N 47 8 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.57 108.50 5.07 0.70 N 48 8 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.49 108.50 4.99 0.70 N 49 9 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 112.94 108.50 4.44 0.70 N 50 9 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.16 108.50 4.66 0.70 N 51 9 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.67 108.50 5.17 0.70 N 52 9 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.66 108.50 5.16 0.70 N 53 9 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.53 108.50 5.03 0.70 N 54 10 "O4'" A U 12 ? ? "C1'" A U 12 ? ? N1 A U 12 ? ? 113.55 108.50 5.05 0.70 N 55 10 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.76 108.50 5.26 0.70 N 56 10 "O4'" A U 14 ? ? "C1'" A U 14 ? ? N1 A U 14 ? ? 113.80 108.50 5.30 0.70 N 57 10 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.59 108.50 5.09 0.70 N 58 10 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.52 108.50 5.02 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LP9 'double helix' 2LP9 'a-form double helix' 2LP9 'hairpin loop' 2LP9 'bulge loop' 2LP9 '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 16 1_555 -0.777 -0.094 0.367 6.716 -9.795 -3.749 1 A_G1:C16_A A 1 ? A 16 ? 19 1 1 A A 2 1_555 A U 15 1_555 -0.750 -0.058 0.064 4.510 -15.143 -4.220 2 A_A2:U15_A A 2 ? A 15 ? 20 1 1 A G 3 1_555 A U 14 1_555 -1.369 -0.246 0.224 6.945 -11.527 -3.980 3 A_G3:U14_A A 3 ? A 14 ? 28 1 1 A G 4 1_555 A C 13 1_555 -0.962 -0.179 0.260 10.786 -9.767 -2.168 4 A_G4:C13_A A 4 ? A 13 ? 19 1 1 A A 5 1_555 A U 12 1_555 -0.801 -0.087 -0.314 -3.293 -15.650 -1.347 5 A_A5:U12_A A 5 ? A 12 ? 20 1 1 A C 6 1_555 A G 10 1_555 1.155 -0.272 -0.073 3.525 -11.055 -1.714 6 A_C6:G10_A A 6 ? A 10 ? 19 1 1 A A 7 1_555 A A 9 1_555 6.605 -1.628 0.836 17.355 23.647 73.144 7 A_A7:A9_A A 7 ? A 9 ? ? ? # 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 16 1_555 A A 2 1_555 A U 15 1_555 -0.264 -1.708 3.191 -0.399 6.271 30.973 -4.215 0.417 2.803 11.594 0.737 31.589 1 AA_G1A2:U15C16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A A 2 1_555 A U 15 1_555 A G 3 1_555 A U 14 1_555 -0.261 -1.858 2.980 -5.890 8.063 29.695 -4.736 -0.460 2.412 15.201 11.104 31.293 2 AA_A2G3:U14U15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A G 3 1_555 A U 14 1_555 A G 4 1_555 A C 13 1_555 -0.110 -1.745 3.016 -4.786 4.586 32.743 -3.712 -0.513 2.742 8.033 8.384 33.389 3 AA_G3G4:C13U14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A C 13 1_555 A A 5 1_555 A U 12 1_555 -0.043 -1.995 3.441 0.537 10.863 32.430 -5.042 0.154 2.653 18.802 -0.930 34.158 4 AA_G4A5:U12C13_AA A 4 ? A 13 ? A 5 ? A 12 ? 1 A A 5 1_555 A U 12 1_555 A C 6 1_555 A G 10 1_555 0.449 -1.149 3.056 -1.767 5.535 42.705 -2.062 -0.769 2.872 7.559 2.414 43.080 5 AA_A5C6:G10U12_AA A 5 ? A 12 ? A 6 ? A 10 ? 1 A C 6 1_555 A G 10 1_555 A A 7 1_555 A A 9 1_555 3.721 2.021 3.045 -8.888 16.019 50.205 1.301 -4.682 2.871 18.198 10.096 53.239 6 AA_C6A7:A9G10_AA A 6 ? A 10 ? A 7 ? A 9 ? #