data_1KPZ # _entry.id 1KPZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 1KPZ pdb_00001kpz 10.2210/pdb1kpz/pdb RCSB RCSB015214 ? ? WWPDB D_1000015214 ? ? # 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 2002-01-11 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-01-24 5 'Structure model' 1 4 2024-05-01 # _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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 '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' citation_author 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list 4 5 'Structure model' chem_comp_atom 5 5 'Structure model' chem_comp_bond 6 5 'Structure model' database_2 7 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_citation_author.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1KPZ _pdbx_database_status.recvd_initial_deposition_date 2002-01-03 _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1KPY _pdbx_database_related.details 'PEMV-1 Structural Ensemble' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nixon, P.L.' 1 'Giedroc, D.P.' 2 # _citation.id primary _citation.title 'Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 322 _citation.page_first 621 _citation.page_last 633 _citation.year 2002 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12225754 _citation.pdbx_database_id_DOI '10.1016/S0022-2836(02)00779-9' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nixon, P.L.' 1 ? primary 'Rangan, A.' 2 ? primary 'Kim, Y.-G.' 3 ? primary 'Rich, A.' 4 ? primary 'Hoffman, D.W.' 5 ? primary 'Hennig, M.' 6 ? primary 'Giedroc, D.P.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'P1-P2 frameshifting pseudoknot' _entity.formula_weight 10640.448 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'Pea Enation Mosaic Virus type I RNA' # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GAAUUCCGGU(CH)GACUCCGGAGAAACAAAGUCAA' _entity_poly.pdbx_seq_one_letter_code_can GAAUUCCGGUCGACUCCGGAGAAACAAAGUCAA _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 A n 1 4 U n 1 5 U n 1 6 C n 1 7 C n 1 8 G n 1 9 G n 1 10 U n 1 11 CH n 1 12 G n 1 13 A n 1 14 C n 1 15 U n 1 16 C n 1 17 C n 1 18 G n 1 19 G n 1 20 A n 1 21 G n 1 22 A n 1 23 A n 1 24 A n 1 25 C n 1 26 A n 1 27 A n 1 28 A n 1 29 G n 1 30 U n 1 31 C n 1 32 A n 1 33 A 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 'Naturally occuring sequence of the P1-P2 frameshifting pseudoknot from Pea Enation Mosaic Virus type I. In vitro SP6 Transcription.' # 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 CH 'RNA linking' n ;N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE ; ? 'C9 H15 N3 O8 P 1' 324.204 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_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 0 ? ? ? A . n A 1 2 A 2 1 ? ? ? A . n A 1 3 A 3 2 ? ? ? A . n A 1 4 U 4 3 ? ? ? A . n A 1 5 U 5 4 4 U URI A . n A 1 6 C 6 5 5 C CYT A . n A 1 7 C 7 6 6 C CYT A . n A 1 8 G 8 7 7 G GUA A . n A 1 9 G 9 8 8 G GUA A . n A 1 10 U 10 9 9 U URI A . n A 1 11 CH 11 10 10 CH CH A . n A 1 12 G 12 11 11 G GUA A . n A 1 13 A 13 12 12 A ADE A . n A 1 14 C 14 13 13 C CYT A . n A 1 15 U 15 14 14 U URI A . n A 1 16 C 16 15 15 C CYT A . n A 1 17 C 17 16 16 C CYT A . n A 1 18 G 18 17 17 G GUA A . n A 1 19 G 19 18 18 G GUA A . n A 1 20 A 20 19 19 A ADE A . n A 1 21 G 21 20 20 G GUA A . n A 1 22 A 22 21 21 A ADE A . n A 1 23 A 23 22 22 A ADE A . n A 1 24 A 24 23 23 A ADE A . n A 1 25 C 25 24 24 C CYT A . n A 1 26 A 26 25 25 A ADE A . n A 1 27 A 27 26 26 A ADE A . n A 1 28 A 28 27 27 A ADE A . n A 1 29 G 29 28 28 G GUA A . n A 1 30 U 30 29 29 U URI A . n A 1 31 C 31 30 30 C CYT A . n A 1 32 A 32 31 31 A ADE A . n A 1 33 A 33 32 ? ? ? A . n # _exptl.entry_id 1KPZ _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.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _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 # _database_PDB_matrix.entry_id 1KPZ _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1KPZ _struct.title 'PEMV-1 P1-P2 Frameshifting Pseudoknot Regularized Average Structure' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1KPZ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Pseudoknot, Frameshifting, Luteovirus, Triple Helix, Protonated Cytidine, Ribonucleic Acid, 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_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1KPZ _struct_ref.pdbx_db_accession 1KPZ _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 1KPZ _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 33 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1KPZ _struct_ref_seq.db_align_beg 0 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 32 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 0 _struct_ref_seq.pdbx_auth_seq_align_end 32 # _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 ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A U 10 "O3'" ? ? ? 1_555 A CH 11 P ? ? A U 9 A CH 10 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale2 covale both ? A CH 11 "O3'" ? ? ? 1_555 A G 12 P ? ? A CH 10 A G 11 1_555 ? ? ? ? ? ? ? 1.652 ? ? hydrog1 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 20 N1 ? ? A U 4 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 20 N6 ? ? A U 4 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A U 5 O2 ? ? ? 1_555 A A 22 N6 ? ? A U 4 A A 21 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog4 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 19 N1 ? ? A C 5 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 19 O6 ? ? A C 5 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 19 N2 ? ? A C 5 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 18 N1 ? ? A C 6 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 18 O6 ? ? A C 6 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 18 N2 ? ? A C 6 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 7 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 7 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 7 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 8 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 8 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 8 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 9 N2 ? ? ? 1_555 A A 27 N1 ? ? A G 8 A A 26 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog17 hydrog ? ? A G 9 N3 ? ? ? 1_555 A A 27 N6 ? ? A G 8 A A 26 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog18 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 28 N7 ? ? A U 9 A A 27 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog19 hydrog ? ? A U 10 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 9 A A 27 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog20 hydrog ? ? A CH 11 O2 ? ? ? 1_555 A A 13 N6 ? ? A CH 10 A A 12 1_555 ? ? ? ? ? ? 'CH-A MISPAIR' ? ? ? hydrog21 hydrog ? ? A CH 11 N4 ? ? ? 1_555 A G 29 N7 ? ? A CH 10 A G 28 1_555 ? ? ? ? ? ? 'CH-G PAIR' ? ? ? hydrog22 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 31 N3 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 31 N4 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A A 13 N6 ? ? ? 1_555 A G 29 O6 ? ? A A 12 A G 28 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog26 hydrog ? ? A A 13 N1 ? ? ? 1_555 A U 30 N3 ? ? A A 12 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A A 13 N6 ? ? ? 1_555 A U 30 O4 ? ? A A 12 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 29 N1 ? ? A C 13 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 29 O6 ? ? A C 13 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 29 N2 ? ? A C 13 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 17 O2 ? ? ? 1_555 A A 26 N6 ? ? A C 16 A A 25 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog32 hydrog ? ? A G 19 N2 ? ? ? 1_555 A A 23 N3 ? ? A G 18 A A 22 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O2 A C 16 ? ? H61 A A 25 ? ? 1.42 2 1 "HO2'" A A 27 ? ? "O4'" A G 28 ? ? 1.53 3 1 "O2'" A C 6 ? ? "O2'" A A 22 ? ? 2.15 # 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 1 "C2'" A U 4 ? ? "C1'" A U 4 ? ? 1.420 1.526 -0.106 0.008 N 2 1 "C2'" A C 5 ? ? "C1'" A C 5 ? ? 1.415 1.526 -0.111 0.008 N 3 1 "C2'" A G 7 ? ? "C1'" A G 7 ? ? 1.396 1.526 -0.130 0.008 N 4 1 "C2'" A G 8 ? ? "C1'" A G 8 ? ? 1.384 1.526 -0.142 0.008 N 5 1 "C2'" A G 11 ? ? "C1'" A G 11 ? ? 1.398 1.526 -0.128 0.008 N 6 1 "C2'" A A 12 ? ? "C1'" A A 12 ? ? 1.396 1.526 -0.130 0.008 N 7 1 "C2'" A C 15 ? ? "C1'" A C 15 ? ? 1.403 1.526 -0.123 0.008 N 8 1 "C2'" A C 16 ? ? "C1'" A C 16 ? ? 1.429 1.526 -0.097 0.008 N 9 1 "C2'" A G 17 ? ? "C1'" A G 17 ? ? 1.390 1.526 -0.136 0.008 N 10 1 "C5'" A G 18 ? ? "C4'" A G 18 ? ? 1.463 1.508 -0.045 0.007 N 11 1 "C2'" A G 18 ? ? "C1'" A G 18 ? ? 1.425 1.526 -0.101 0.008 N 12 1 "C2'" A A 19 ? ? "C1'" A A 19 ? ? 1.378 1.526 -0.148 0.008 N 13 1 C8 A A 19 ? ? N9 A A 19 ? ? 1.324 1.373 -0.049 0.008 N 14 1 C2 A A 21 ? ? N3 A A 21 ? ? 1.235 1.331 -0.096 0.009 N 15 1 N3 A A 21 ? ? C4 A A 21 ? ? 1.283 1.344 -0.061 0.006 N 16 1 C4 A A 21 ? ? C5 A A 21 ? ? 1.322 1.383 -0.061 0.007 N 17 1 C8 A A 21 ? ? N9 A A 21 ? ? 1.314 1.373 -0.059 0.008 N 18 1 N9 A A 21 ? ? C4 A A 21 ? ? 1.302 1.374 -0.072 0.006 N 19 1 N1 A C 24 ? ? C6 A C 24 ? ? 1.413 1.367 0.046 0.006 N 20 1 "C2'" A G 28 ? ? "C1'" A G 28 ? ? 1.394 1.526 -0.132 0.008 N 21 1 "C2'" A U 29 ? ? "C1'" A U 29 ? ? 1.458 1.526 -0.068 0.008 N 22 1 "C2'" A C 30 ? ? "C1'" A C 30 ? ? 1.457 1.526 -0.069 0.008 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 1 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.52 108.50 5.02 0.70 N 2 1 "O4'" A C 5 ? ? "C1'" A C 5 ? ? N1 A C 5 ? ? 112.79 108.50 4.29 0.70 N 3 1 C6 A C 5 ? ? N1 A C 5 ? ? C2 A C 5 ? ? 117.72 120.30 -2.58 0.40 N 4 1 N1 A C 5 ? ? C2 A C 5 ? ? O2 A C 5 ? ? 122.62 118.90 3.72 0.60 N 5 1 "C1'" A C 6 ? ? "O4'" A C 6 ? ? "C4'" A C 6 ? ? 104.99 109.70 -4.71 0.70 N 6 1 "C4'" A C 6 ? ? "C3'" A C 6 ? ? "C2'" A C 6 ? ? 95.72 102.60 -6.88 1.00 N 7 1 "O4'" A C 6 ? ? "C1'" A C 6 ? ? N1 A C 6 ? ? 114.14 108.50 5.64 0.70 N 8 1 "C3'" A G 7 ? ? "C2'" A G 7 ? ? "C1'" A G 7 ? ? 96.04 101.30 -5.26 0.70 N 9 1 "O4'" A G 7 ? ? "C1'" A G 7 ? ? N9 A G 7 ? ? 115.64 108.50 7.14 0.70 N 10 1 N7 A G 7 ? ? C8 A G 7 ? ? N9 A G 7 ? ? 118.01 113.10 4.91 0.50 N 11 1 C8 A G 7 ? ? N9 A G 7 ? ? C4 A G 7 ? ? 102.48 106.40 -3.92 0.40 N 12 1 N7 A G 8 ? ? C8 A G 8 ? ? N9 A G 8 ? ? 118.15 113.10 5.05 0.50 N 13 1 C8 A G 8 ? ? N9 A G 8 ? ? C4 A G 8 ? ? 102.80 106.40 -3.60 0.40 N 14 1 "C3'" A U 9 ? ? "C2'" A U 9 ? ? "C1'" A U 9 ? ? 106.68 101.50 5.18 0.80 N 15 1 "O4'" A G 11 ? ? "C1'" A G 11 ? ? N9 A G 11 ? ? 115.19 108.50 6.69 0.70 N 16 1 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 118.13 113.10 5.03 0.50 N 17 1 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 102.71 106.40 -3.69 0.40 N 18 1 "C1'" A A 12 ? ? "O4'" A A 12 ? ? "C4'" A A 12 ? ? 105.30 109.70 -4.40 0.70 N 19 1 "C3'" A A 12 ? ? "C2'" A A 12 ? ? "C1'" A A 12 ? ? 96.17 101.30 -5.13 0.70 N 20 1 "O4'" A A 12 ? ? "C1'" A A 12 ? ? N9 A A 12 ? ? 113.23 108.50 4.73 0.70 N 21 1 N7 A A 12 ? ? C8 A A 12 ? ? N9 A A 12 ? ? 118.22 113.80 4.42 0.50 N 22 1 "C3'" A C 13 ? ? "C2'" A C 13 ? ? "C1'" A C 13 ? ? 106.61 101.50 5.11 0.80 N 23 1 "C3'" A U 14 ? ? "C2'" A U 14 ? ? "C1'" A U 14 ? ? 106.48 101.50 4.98 0.80 N 24 1 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 113.66 108.50 5.16 0.70 N 25 1 "C5'" A G 17 ? ? "C4'" A G 17 ? ? "O4'" A G 17 ? ? 100.77 109.10 -8.33 1.20 N 26 1 "O4'" A G 17 ? ? "C1'" A G 17 ? ? N9 A G 17 ? ? 117.50 108.50 9.00 0.70 N 27 1 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 118.13 113.10 5.03 0.50 N 28 1 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 102.20 106.40 -4.20 0.40 N 29 1 "O4'" A G 18 ? ? "C1'" A G 18 ? ? N9 A G 18 ? ? 116.49 108.50 7.99 0.70 N 30 1 N7 A G 18 ? ? C8 A G 18 ? ? N9 A G 18 ? ? 118.61 113.10 5.51 0.50 N 31 1 C8 A G 18 ? ? N9 A G 18 ? ? C4 A G 18 ? ? 101.23 106.40 -5.17 0.40 N 32 1 "C5'" A A 19 ? ? "C4'" A A 19 ? ? "O4'" A A 19 ? ? 97.98 109.10 -11.12 1.20 N 33 1 "O4'" A A 19 ? ? "C1'" A A 19 ? ? N9 A A 19 ? ? 117.74 108.50 9.24 0.70 N 34 1 N7 A A 19 ? ? C8 A A 19 ? ? N9 A A 19 ? ? 120.14 113.80 6.34 0.50 N 35 1 C8 A A 19 ? ? N9 A A 19 ? ? C4 A A 19 ? ? 101.04 105.80 -4.76 0.40 N 36 1 N7 A G 20 ? ? C8 A G 20 ? ? N9 A G 20 ? ? 117.81 113.10 4.71 0.50 N 37 1 C8 A G 20 ? ? N9 A G 20 ? ? C4 A G 20 ? ? 103.29 106.40 -3.11 0.40 N 38 1 N3 A A 21 ? ? C4 A A 21 ? ? C5 A A 21 ? ? 131.45 126.80 4.65 0.70 N 39 1 C5 A A 21 ? ? N7 A A 21 ? ? C8 A A 21 ? ? 99.20 103.90 -4.70 0.50 N 40 1 N7 A A 21 ? ? C8 A A 21 ? ? N9 A A 21 ? ? 118.07 113.80 4.27 0.50 N 41 1 C8 A A 21 ? ? N9 A A 21 ? ? C4 A A 21 ? ? 102.76 105.80 -3.04 0.40 N 42 1 N9 A A 21 ? ? C4 A A 21 ? ? C5 A A 21 ? ? 109.37 105.80 3.57 0.40 N 43 1 N3 A A 21 ? ? C4 A A 21 ? ? N9 A A 21 ? ? 119.12 127.40 -8.28 0.80 N 44 1 "O4'" A A 22 ? ? "C1'" A A 22 ? ? N9 A A 22 ? ? 102.50 108.20 -5.70 0.80 N 45 1 N7 A A 22 ? ? C8 A A 22 ? ? N9 A A 22 ? ? 117.62 113.80 3.82 0.50 N 46 1 C8 A A 22 ? ? N9 A A 22 ? ? C4 A A 22 ? ? 102.58 105.80 -3.22 0.40 N 47 1 N7 A A 23 ? ? C8 A A 23 ? ? N9 A A 23 ? ? 117.33 113.80 3.53 0.50 N 48 1 "C3'" A C 24 ? ? "C2'" A C 24 ? ? "C1'" A C 24 ? ? 106.46 101.50 4.96 0.80 N 49 1 "O4'" A A 25 ? ? "C1'" A A 25 ? ? N9 A A 25 ? ? 114.12 108.50 5.62 0.70 N 50 1 N7 A A 25 ? ? C8 A A 25 ? ? N9 A A 25 ? ? 116.91 113.80 3.11 0.50 N 51 1 "C3'" A A 26 ? ? "C2'" A A 26 ? ? "C1'" A A 26 ? ? 106.41 101.50 4.91 0.80 N 52 1 N7 A A 26 ? ? C8 A A 26 ? ? N9 A A 26 ? ? 117.52 113.80 3.72 0.50 N 53 1 N7 A A 27 ? ? C8 A A 27 ? ? N9 A A 27 ? ? 116.97 113.80 3.17 0.50 N 54 1 "C5'" A G 28 ? ? "C4'" A G 28 ? ? "O4'" A G 28 ? ? 101.86 109.10 -7.24 1.20 N 55 1 "C3'" A G 28 ? ? "C2'" A G 28 ? ? "C1'" A G 28 ? ? 96.36 101.30 -4.94 0.70 N 56 1 "O4'" A G 28 ? ? "C1'" A G 28 ? ? N9 A G 28 ? ? 116.43 108.50 7.93 0.70 N 57 1 N7 A G 28 ? ? C8 A G 28 ? ? N9 A G 28 ? ? 118.06 113.10 4.96 0.50 N 58 1 C8 A G 28 ? ? N9 A G 28 ? ? C4 A G 28 ? ? 102.26 106.40 -4.14 0.40 N 59 1 "C4'" A U 29 ? ? "C3'" A U 29 ? ? "C2'" A U 29 ? ? 94.33 102.60 -8.27 1.00 N 60 1 N1 A C 30 ? ? "C1'" A C 30 ? ? "C2'" A C 30 ? ? 125.77 114.00 11.77 1.30 N 61 1 "C3'" A A 31 ? ? "C2'" A A 31 ? ? "C1'" A A 31 ? ? 106.30 101.50 4.80 0.80 N 62 1 N7 A A 31 ? ? C8 A A 31 ? ? N9 A A 31 ? ? 117.49 113.80 3.69 0.50 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 U A 4 ? ? 0.116 'SIDE CHAIN' 2 1 C A 5 ? ? 0.098 'SIDE CHAIN' 3 1 C A 6 ? ? 0.088 'SIDE CHAIN' 4 1 G A 7 ? ? 0.087 'SIDE CHAIN' 5 1 G A 8 ? ? 0.115 'SIDE CHAIN' 6 1 U A 9 ? ? 0.114 'SIDE CHAIN' 7 1 G A 11 ? ? 0.079 'SIDE CHAIN' 8 1 A A 12 ? ? 0.101 'SIDE CHAIN' 9 1 C A 15 ? ? 0.099 'SIDE CHAIN' 10 1 C A 16 ? ? 0.098 'SIDE CHAIN' 11 1 G A 17 ? ? 0.093 'SIDE CHAIN' 12 1 G A 18 ? ? 0.108 'SIDE CHAIN' 13 1 A A 19 ? ? 0.078 'SIDE CHAIN' 14 1 A A 21 ? ? 0.210 'SIDE CHAIN' 15 1 A A 22 ? ? 0.142 'SIDE CHAIN' 16 1 A A 25 ? ? 0.057 'SIDE CHAIN' 17 1 A A 26 ? ? 0.060 'SIDE CHAIN' 18 1 G A 28 ? ? 0.090 'SIDE CHAIN' 19 1 U A 29 ? ? 0.105 'SIDE CHAIN' 20 1 C A 30 ? ? 0.165 'SIDE CHAIN' # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id CH _pdbx_struct_mod_residue.label_seq_id 11 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id CH _pdbx_struct_mod_residue.auth_seq_id 10 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id C _pdbx_struct_mod_residue.details ;N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE ; # _pdbx_nmr_ensemble.entry_id 1KPZ _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? # _pdbx_nmr_representative.entry_id 1KPZ _pdbx_nmr_representative.conformer_id ? _pdbx_nmr_representative.selection_criteria 'minimized average structure' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '2 mM PEMV-1 RNA' _pdbx_nmr_sample_details.solvent_system '10 mM KPO4, pH 6.0, 100 mM KCl, 5 mM MgCl2' # 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 1 283 atmospheric 6.0 '100 mM KCl, 5 mM MgCl2' atm K 2 298 atmospheric 6.0 '100 mM KCl, 5 mM MgCl2' atm K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 2 '2D NOESY' 1 # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'structure solution' X-PLOR 3.851 'Brunger, A.T' 1 refinement X-PLOR 3.851 'Brunger, A.T' 2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A G 0 ? A G 1 2 1 Y 1 A A 1 ? A A 2 3 1 Y 1 A A 2 ? A A 3 4 1 Y 1 A U 3 ? A U 4 5 1 Y 1 A A 32 ? A A 33 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CH OP3 O N N 73 CH P P N N 74 CH OP1 O N N 75 CH OP2 O N N 76 CH "O5'" O N N 77 CH "C5'" C N N 78 CH "C4'" C N R 79 CH "O4'" O N N 80 CH "C3'" C N S 81 CH "O3'" O N N 82 CH "C2'" C N R 83 CH "O2'" O N N 84 CH "C1'" C N R 85 CH N1 N N N 86 CH C2 C N N 87 CH O2 O N N 88 CH N3 N N N 89 CH C4 C N N 90 CH N4 N N N 91 CH C5 C N N 92 CH C6 C N N 93 CH HOP3 H N N 94 CH HOP2 H N N 95 CH "H5'" H N N 96 CH "H5''" H N N 97 CH "H4'" H N N 98 CH "H3'" H N N 99 CH "HO3'" H N N 100 CH "H2'" H N N 101 CH "HO2'" H N N 102 CH "H1'" H N N 103 CH HN3 H N N 104 CH H41 H N N 105 CH H42 H N N 106 CH H5 H N N 107 CH H6 H N N 108 G OP3 O N N 109 G P P N N 110 G OP1 O N N 111 G OP2 O N N 112 G "O5'" O N N 113 G "C5'" C N N 114 G "C4'" C N R 115 G "O4'" O N N 116 G "C3'" C N S 117 G "O3'" O N N 118 G "C2'" C N R 119 G "O2'" O N N 120 G "C1'" C N R 121 G N9 N Y N 122 G C8 C Y N 123 G N7 N Y N 124 G C5 C Y N 125 G C6 C N N 126 G O6 O N N 127 G N1 N N N 128 G C2 C N N 129 G N2 N N N 130 G N3 N N N 131 G C4 C Y N 132 G HOP3 H N N 133 G HOP2 H N N 134 G "H5'" H N N 135 G "H5''" H N N 136 G "H4'" H N N 137 G "H3'" H N N 138 G "HO3'" H N N 139 G "H2'" H N N 140 G "HO2'" H N N 141 G "H1'" H N N 142 G H8 H N N 143 G H1 H N N 144 G H21 H N N 145 G H22 H N N 146 U OP3 O N N 147 U P P N N 148 U OP1 O N N 149 U OP2 O N N 150 U "O5'" O N N 151 U "C5'" C N N 152 U "C4'" C N R 153 U "O4'" O N N 154 U "C3'" C N S 155 U "O3'" O N N 156 U "C2'" C N R 157 U "O2'" O N N 158 U "C1'" C N R 159 U N1 N N N 160 U C2 C N N 161 U O2 O N N 162 U N3 N N N 163 U C4 C N N 164 U O4 O N N 165 U C5 C N N 166 U C6 C N N 167 U HOP3 H N N 168 U HOP2 H N N 169 U "H5'" H N N 170 U "H5''" H N N 171 U "H4'" H N N 172 U "H3'" H N N 173 U "HO3'" H N N 174 U "H2'" H N N 175 U "HO2'" H N N 176 U "H1'" H N N 177 U H3 H N N 178 U H5 H N N 179 U H6 H N N 180 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 CH OP3 P sing N N 76 CH OP3 HOP3 sing N N 77 CH P OP1 doub N N 78 CH P OP2 sing N N 79 CH P "O5'" sing N N 80 CH OP2 HOP2 sing N N 81 CH "O5'" "C5'" sing N N 82 CH "C5'" "C4'" sing N N 83 CH "C5'" "H5'" sing N N 84 CH "C5'" "H5''" sing N N 85 CH "C4'" "O4'" sing N N 86 CH "C4'" "C3'" sing N N 87 CH "C4'" "H4'" sing N N 88 CH "O4'" "C1'" sing N N 89 CH "C3'" "O3'" sing N N 90 CH "C3'" "C2'" sing N N 91 CH "C3'" "H3'" sing N N 92 CH "O3'" "HO3'" sing N N 93 CH "C2'" "O2'" sing N N 94 CH "C2'" "C1'" sing N N 95 CH "C2'" "H2'" sing N N 96 CH "O2'" "HO2'" sing N N 97 CH "C1'" N1 sing N N 98 CH "C1'" "H1'" sing N N 99 CH N1 C2 sing N N 100 CH N1 C6 doub N N 101 CH C2 O2 doub N N 102 CH C2 N3 sing N N 103 CH N3 C4 sing N N 104 CH N3 HN3 sing N N 105 CH C4 N4 sing N N 106 CH C4 C5 doub N N 107 CH N4 H41 sing N N 108 CH N4 H42 sing N N 109 CH C5 C6 sing N N 110 CH C5 H5 sing N N 111 CH C6 H6 sing N N 112 G OP3 P sing N N 113 G OP3 HOP3 sing N N 114 G P OP1 doub N N 115 G P OP2 sing N N 116 G P "O5'" sing N N 117 G OP2 HOP2 sing N N 118 G "O5'" "C5'" sing N N 119 G "C5'" "C4'" sing N N 120 G "C5'" "H5'" sing N N 121 G "C5'" "H5''" sing N N 122 G "C4'" "O4'" sing N N 123 G "C4'" "C3'" sing N N 124 G "C4'" "H4'" sing N N 125 G "O4'" "C1'" sing N N 126 G "C3'" "O3'" sing N N 127 G "C3'" "C2'" sing N N 128 G "C3'" "H3'" sing N N 129 G "O3'" "HO3'" sing N N 130 G "C2'" "O2'" sing N N 131 G "C2'" "C1'" sing N N 132 G "C2'" "H2'" sing N N 133 G "O2'" "HO2'" sing N N 134 G "C1'" N9 sing N N 135 G "C1'" "H1'" sing N N 136 G N9 C8 sing Y N 137 G N9 C4 sing Y N 138 G C8 N7 doub Y N 139 G C8 H8 sing N N 140 G N7 C5 sing Y N 141 G C5 C6 sing N N 142 G C5 C4 doub Y N 143 G C6 O6 doub N N 144 G C6 N1 sing N N 145 G N1 C2 sing N N 146 G N1 H1 sing N N 147 G C2 N2 sing N N 148 G C2 N3 doub N N 149 G N2 H21 sing N N 150 G N2 H22 sing N N 151 G N3 C4 sing N N 152 U OP3 P sing N N 153 U OP3 HOP3 sing N N 154 U P OP1 doub N N 155 U P OP2 sing N N 156 U P "O5'" sing N N 157 U OP2 HOP2 sing N N 158 U "O5'" "C5'" sing N N 159 U "C5'" "C4'" sing N N 160 U "C5'" "H5'" sing N N 161 U "C5'" "H5''" sing N N 162 U "C4'" "O4'" sing N N 163 U "C4'" "C3'" sing N N 164 U "C4'" "H4'" sing N N 165 U "O4'" "C1'" sing N N 166 U "C3'" "O3'" sing N N 167 U "C3'" "C2'" sing N N 168 U "C3'" "H3'" sing N N 169 U "O3'" "HO3'" sing N N 170 U "C2'" "O2'" sing N N 171 U "C2'" "C1'" sing N N 172 U "C2'" "H2'" sing N N 173 U "O2'" "HO2'" sing N N 174 U "C1'" N1 sing N N 175 U "C1'" "H1'" sing N N 176 U N1 C2 sing N N 177 U N1 C6 sing N N 178 U C2 O2 doub N N 179 U C2 N3 sing N N 180 U N3 C4 sing N N 181 U N3 H3 sing N N 182 U C4 O4 doub N N 183 U C4 C5 sing N N 184 U C5 C6 doub N N 185 U C5 H5 sing N N 186 U C6 H6 sing N N 187 # _ndb_struct_conf_na.entry_id 1KPZ _ndb_struct_conf_na.feature 'quadruple helix' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 INOVA Varian 500 ? 2 INOVA Varian 600 ? # _atom_sites.entry_id 1KPZ _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_