data_2KPD # _entry.id 2KPD # _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 2KPD pdb_00002kpd 10.2210/pdb2kpd/pdb RCSB RCSB101406 ? ? WWPDB D_1000101406 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2KPC _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KPD _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-10-12 _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 'Lescrinier, E.' 1 'Dyubankova, N.' 2 'Nauwelaerts, K.' 3 'Jones, R.' 4 'Herdewijn, P.' 5 # _citation.id primary _citation.title ;Structure Determination of the Top-Loop of the Conserved 3'-Terminal Secondary Structure in the Genome of Flaviviruses. ; _citation.journal_abbrev Chembiochem _citation.journal_volume 11 _citation.page_first 1404 _citation.page_last 1412 _citation.year 2010 _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 20540055 _citation.pdbx_database_id_DOI 10.1002/cbic.200900765 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lescrinier, E.' 1 ? primary 'Dyubankova, N.' 2 ? primary 'Nauwelaerts, K.' 3 ? primary 'Jones, R.' 4 ? primary 'Herdewijn, P.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*UP*GP*AP*GP*CP*UP*CP*AP*GP*UP*UP*UP*GP*CP*UP*CP*A)-3') ; _entity.formula_weight 5381.205 _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 UGAGCUCAGUUUGCUCA _entity_poly.pdbx_seq_one_letter_code_can UGAGCUCAGUUUGCUCA _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 U n 1 2 G n 1 3 A n 1 4 G n 1 5 C n 1 6 U n 1 7 C n 1 8 A n 1 9 G n 1 10 U n 1 11 U n 1 12 U n 1 13 G n 1 14 C n 1 15 U n 1 16 C n 1 17 A n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2KPD _struct_ref.pdbx_db_accession 2KPD _struct_ref.entity_id 1 _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 2KPD _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 17 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2KPD _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 17 _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 17 # 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-13C HSQC' 1 2 1 '2D DQF-COSY' 1 3 1 '2D 1H-1H TOCSY' 1 4 1 '2D 1H-1H NOESY' 1 5 1 '2D 1H-31P-COSY' 2 6 1 '2D 1H-1H NOESY' 2 7 2 '2D 1H-1H NOESY' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 ? 5.0 ambient ? 295 K 2 ? 5.0 ambient ? 283 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1-2 mM RNA, 100% D2O' 1 '100% D2O' '1-2 mM RNA, 100% D2O' 2 '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 600 Bruker AVANCE 1 'Bruker Avance' 500 Bruker AVANCE 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2KPD _pdbx_nmr_refine.method 'torsion angle dynamics, simulated annealing' _pdbx_nmr_refine.details 'in water box' _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 'all calculated structures submitted' _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KPD _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 2KPD _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Schwieters, C.D. et al.' refinement 'X-PLOR NIH' ? 1 'Keller, R. et al.' 'data analysis' CARA ? 2 'Bruker Biospin' collection TopSpin ? 3 # _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 2KPD _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KPD _struct.title 'Structure determination of the top-loop of the conserved 3 terminal secondary structure in the genome of YFV-mutant' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KPD _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;yellow fever virus mutant, 3'-terminal loop, genome, 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 U 1 N3 ? ? ? 1_555 A A 17 N1 ? ? A U 1 A A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A U 1 O4 ? ? ? 1_555 A A 17 N6 ? ? A U 1 A A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 2 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 2 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 2 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 15 N3 ? ? A A 3 A U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 15 O4 ? ? A A 3 A U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 4 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 4 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 4 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 13 N1 ? ? A C 5 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 13 O6 ? ? A C 5 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 13 N2 ? ? A C 5 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 O4 ? ? ? 1_555 A U 12 N3 ? ? A U 6 A U 12 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog15 hydrog ? ? A C 7 O2 ? ? ? 1_555 A U 11 N3 ? ? A C 7 A U 11 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2KPD _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 U 1 1 1 U U A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 C 5 5 5 C C 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 A 8 8 8 A A A . n A 1 9 G 9 9 9 G G A . n A 1 10 U 10 10 10 U U A . n A 1 11 U 11 11 11 U U A . n A 1 12 U 12 12 12 U U A . n A 1 13 G 13 13 13 G G A . n A 1 14 C 14 14 14 C C A . n A 1 15 U 15 15 15 U U A . n A 1 16 C 16 16 16 C C A . n A 1 17 A 17 17 17 A A 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 2010-06-30 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_nmr_spectrometer 4 3 'Structure model' pdbx_struct_assembly 5 3 '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 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' '_pdbx_nmr_spectrometer.model' # 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 ? 1-2 mM ? 1 RNA ? 1-2 mM ? 2 # 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 H61 A A 3 ? ? O4 A U 15 ? ? 1.42 2 1 O6 A G 4 ? ? H41 A C 14 ? ? 1.45 3 1 O6 A G 2 ? ? H41 A C 16 ? ? 1.48 4 1 H1 A G 4 ? ? N3 A C 14 ? ? 1.58 5 2 "HO2'" A C 5 ? ? "O5'" A U 6 ? ? 1.43 6 2 "HO2'" A U 11 ? ? "O5'" A U 12 ? ? 1.55 7 2 H21 A G 2 ? ? O2 A C 16 ? ? 1.55 8 3 "HO2'" A G 13 ? ? "O4'" A C 14 ? ? 1.31 9 3 "HO2'" A U 10 ? ? OP2 A U 11 ? ? 1.37 10 3 H21 A G 4 ? ? O2 A C 14 ? ? 1.38 11 3 "HO2'" A C 5 ? ? "O5'" A U 6 ? ? 1.39 12 3 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.45 13 3 "HO2'" A C 14 ? ? "O5'" A U 15 ? ? 1.49 14 3 H21 A G 2 ? ? O2 A C 16 ? ? 1.52 15 4 "HO2'" A U 11 ? ? "O4'" A U 12 ? ? 1.29 16 4 "HO2'" A G 2 ? ? "O4'" A A 3 ? ? 1.57 17 5 H21 A G 2 ? ? O2 A C 16 ? ? 1.35 18 5 H21 A G 4 ? ? O2 A C 14 ? ? 1.36 19 5 "HO2'" A A 3 ? ? "O4'" A G 4 ? ? 1.44 20 5 H1 A G 2 ? ? N3 A C 16 ? ? 1.51 21 5 O6 A G 2 ? ? H41 A C 16 ? ? 1.51 22 5 "HO2'" A U 10 ? ? OP1 A U 11 ? ? 1.55 23 5 H1 A G 4 ? ? N3 A C 14 ? ? 1.59 24 6 "HO2'" A A 3 ? ? "O4'" A G 4 ? ? 1.34 25 6 "HO2'" A C 14 ? ? "O4'" A U 15 ? ? 1.56 26 6 "O5'" A U 10 ? ? H5 A U 11 ? ? 1.56 27 7 "HO2'" A U 12 ? ? OP2 A G 13 ? ? 1.41 28 7 H61 A A 3 ? ? O4 A U 15 ? ? 1.52 29 7 H21 A G 4 ? ? O2 A C 14 ? ? 1.53 30 7 H21 A G 2 ? ? O2 A C 16 ? ? 1.53 31 7 O2 A C 5 ? ? H21 A G 13 ? ? 1.57 32 8 O2 A C 5 ? ? H21 A G 13 ? ? 1.40 33 8 "HO2'" A A 3 ? ? "O4'" A G 4 ? ? 1.47 34 8 O6 A G 2 ? ? H41 A C 16 ? ? 1.48 35 8 "HO2'" A U 11 ? ? "O5'" A U 12 ? ? 1.53 36 9 H61 A A 3 ? ? O4 A U 15 ? ? 1.33 37 9 O2 A C 5 ? ? H21 A G 13 ? ? 1.43 38 9 H1 A G 2 ? ? N3 A C 16 ? ? 1.47 39 9 O6 A G 2 ? ? H41 A C 16 ? ? 1.48 40 9 H3 A U 6 ? ? O4 A U 12 ? ? 1.51 41 9 H21 A G 4 ? ? O2 A C 14 ? ? 1.51 42 9 "HO2'" A U 11 ? ? "O5'" A U 12 ? ? 1.52 43 9 H21 A G 2 ? ? O2 A C 16 ? ? 1.55 44 10 H3 A U 6 ? ? O4 A U 12 ? ? 1.37 45 10 O2 A C 5 ? ? H21 A G 13 ? ? 1.44 46 10 O2 A U 6 ? ? H3 A U 12 ? ? 1.55 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 5 C4 A A 3 ? ? C5 A A 3 ? ? 1.340 1.383 -0.043 0.007 N 2 8 N3 A A 3 ? ? C4 A A 3 ? ? 1.383 1.344 0.039 0.006 N # 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 4 N1 A A 3 ? ? C2 A A 3 ? ? N3 A A 3 ? ? 125.89 129.30 -3.41 0.50 N 2 5 N1 A A 3 ? ? C2 A A 3 ? ? N3 A A 3 ? ? 125.57 129.30 -3.73 0.50 N 3 6 "O4'" A A 3 ? ? "C1'" A A 3 ? ? N9 A A 3 ? ? 112.98 108.50 4.48 0.70 N 4 7 N1 A A 3 ? ? C2 A A 3 ? ? N3 A A 3 ? ? 126.26 129.30 -3.04 0.50 N 5 8 N1 A A 3 ? ? C2 A A 3 ? ? N3 A A 3 ? ? 126.27 129.30 -3.03 0.50 N 6 10 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 113.01 108.50 4.51 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2KPD 'double helix' 2KPD 'a-form double helix' 2KPD 'hairpin loop' 2KPD '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 U 1 1_555 A A 17 1_555 -1.961 -0.976 -2.031 5.010 6.638 -20.977 1 A_U1:A17_A A 1 ? A 17 ? 20 1 1 A G 2 1_555 A C 16 1_555 -0.335 -0.295 -0.167 -10.117 -23.043 -13.741 2 A_G2:C16_A A 2 ? A 16 ? 19 1 1 A A 3 1_555 A U 15 1_555 0.312 -0.268 -0.874 -17.218 -12.274 -9.928 3 A_A3:U15_A A 3 ? A 15 ? 20 1 1 A G 4 1_555 A C 14 1_555 -0.016 -0.446 -0.312 -13.296 -6.552 -4.242 4 A_G4:C14_A A 4 ? A 14 ? 19 1 1 A C 5 1_555 A G 13 1_555 1.045 -0.368 -0.664 -5.505 -18.279 11.448 5 A_C5:G13_A A 5 ? A 13 ? 19 1 1 A U 6 1_555 A U 12 1_555 -1.591 -1.828 1.033 8.103 14.012 -12.261 6 A_U6:U12_A A 6 ? A 12 ? ? ? 1 A C 7 1_555 A U 11 1_555 2.841 -2.363 -1.572 36.196 19.233 6.369 7 A_C7:U11_A A 7 ? A 11 ? ? ? # 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 U 1 1_555 A A 17 1_555 A G 2 1_555 A C 16 1_555 0.381 -1.553 4.292 -6.840 7.660 43.524 -2.931 -1.294 3.879 10.162 9.074 44.662 1 AA_U1G2:C16A17_AA A 1 ? A 17 ? A 2 ? A 16 ? 1 A G 2 1_555 A C 16 1_555 A A 3 1_555 A U 15 1_555 0.160 -1.845 3.552 3.369 5.813 32.221 -4.290 0.316 3.180 10.334 -5.990 32.896 2 AA_G2A3:U15C16_AA A 2 ? A 16 ? A 3 ? A 15 ? 1 A A 3 1_555 A U 15 1_555 A G 4 1_555 A C 14 1_555 0.958 -1.167 3.692 -1.186 -6.327 30.578 -0.776 -2.041 3.812 -11.832 2.219 31.232 3 AA_A3G4:C14U15_AA A 3 ? A 15 ? A 4 ? A 14 ? 1 A G 4 1_555 A C 14 1_555 A C 5 1_555 A G 13 1_555 0.409 -1.539 2.952 6.969 11.130 24.144 -5.502 0.552 2.091 24.431 -15.298 27.438 4 AA_G4C5:G13C14_AA A 4 ? A 14 ? A 5 ? A 13 ? 1 A C 5 1_555 A G 13 1_555 A U 6 1_555 A U 12 1_555 -1.043 -0.449 3.404 -19.834 -7.581 32.871 0.384 -1.203 3.488 -11.969 31.315 38.973 5 AA_C5U6:U12G13_AA A 5 ? A 13 ? A 6 ? A 12 ? 1 A U 6 1_555 A U 12 1_555 A C 7 1_555 A U 11 1_555 1.782 -0.919 2.661 12.711 -8.037 49.620 -0.563 -1.268 3.105 -9.332 -14.759 51.711 6 AA_U6C7:U11U12_AA A 6 ? A 12 ? A 7 ? A 11 ? #