data_2LVY # _entry.id 2LVY # _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 2LVY pdb_00002lvy 10.2210/pdb2lvy/pdb RCSB RCSB102899 ? ? BMRB 18593 ? 10.13018/BMR18593 WWPDB D_1000102899 ? ? # 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 2013-04-10 2 'Structure model' 1 1 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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' pdbx_nmr_software 5 2 'Structure model' pdbx_nmr_spectrometer 6 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_nmr_software.name' 4 2 'Structure model' '_pdbx_nmr_spectrometer.model' 5 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LVY _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-07-13 _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 ? # _pdbx_database_related.db_id 18593 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _audit_author.name 'Baraguey, C.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure. ; _citation.journal_abbrev Org.Biomol.Chem. _citation.journal_volume 11 _citation.page_first 2638 _citation.page_last 2647 _citation.year 2013 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1477-0520 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23455628 _citation.pdbx_database_id_DOI 10.1039/c3ob27005j # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Baraguey, C.' 1 ? primary 'Lescrinier, E.' 2 ? primary 'Lavergne, T.' 3 ? primary 'Debart, F.' 4 ? primary 'Herdewijn, P.' 5 ? primary 'Vasseur, J.J.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3') ; 2919.889 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*CP*GP*UP*AP*GP*CP*GP*T)-3') ; 2885.794 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes 'CGC(UPV)ACGC(DT)' CGCXACGCT A ? 2 polyribonucleotide no no 'GCGUAGCG(DT)' GCGUAGCGT B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 C n 1 4 UPV n 1 5 A n 1 6 C n 1 7 G n 1 8 C n 1 9 DT n 2 1 G n 2 2 C n 2 3 G n 2 4 U n 2 5 A n 2 6 G n 2 7 C n 2 8 G n 2 9 DT n # 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 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 UPV 'RNA linking' n ;2'-O-{[(2,2-dimethylpropanoyl)oxy]methyl}uridine 5'-(dihydrogen phosphate) ; ? 'C15 H23 N2 O11 P' 438.324 # 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 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 UPV 4 4 4 UPV UPV 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 G 7 7 7 G G A . n A 1 8 C 8 8 8 C C A . n A 1 9 DT 9 9 9 DT DT A . n B 2 1 G 1 10 10 G G B . n B 2 2 C 2 11 11 C C B . n B 2 3 G 3 12 12 G G B . n B 2 4 U 4 13 13 U U B . n B 2 5 A 5 14 14 A A B . n B 2 6 G 6 15 15 G G B . n B 2 7 C 7 16 16 C C B . n B 2 8 G 8 17 17 G G B . n B 2 9 DT 9 18 18 DT DT B . n # _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 2LVY _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LVY _struct.title ;Solution Structure of a RNA Duplex Containing a 2'-O-Pivaloyloxymethyl Modification ; _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LVY _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, modification' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2LVY 2LVY 1 ? ? ? 2 PDB 2LVY 2LVY 2 ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2LVY A 1 ? 9 ? 2LVY 1 ? 9 ? 1 9 2 2 2LVY B 1 ? 9 ? 2LVY 10 ? 18 ? 10 18 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _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 covale1 covale both ? A C 3 "O3'" ? ? ? 1_555 A UPV 4 P ? ? A C 3 A UPV 4 1_555 ? ? ? ? ? ? ? 1.610 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 1 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 1 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 1 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 1 N4 ? ? ? 1_555 B DT 9 O4 ? ? A C 1 B DT 18 1_555 ? ? ? ? ? ? 'C-DT MISPAIR' ? ? ? hydrog5 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 2 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 2 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 2 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 5 B U 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 5 B U 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 B U 4 N3 ? ? A C 6 B U 13 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 B U 4 O4 ? ? A C 6 B U 13 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 2 O2 ? ? A G 7 B C 11 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog16 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B G 1 N1 ? ? A DT 9 B G 10 1_555 ? ? ? ? ? ? 'DT-G 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 6 "HO2'" B A 14 ? ? "O4'" B G 15 ? ? 1.53 2 7 "HO2'" A A 5 ? ? "O4'" A C 6 ? ? 1.59 3 9 H21 A G 2 ? ? O2 B C 16 ? ? 1.56 4 12 "HO2'" B A 14 ? ? "O4'" B G 15 ? ? 1.55 5 13 O2 A C 8 ? ? H21 B G 10 ? ? 1.60 6 14 O2 A C 1 ? ? H21 B G 17 ? ? 1.56 7 16 O2 A C 3 ? ? H22 B G 15 ? ? 1.58 8 17 "HO2'" B A 14 ? ? "O4'" B G 15 ? ? 1.55 9 17 "HO2'" A C 3 ? ? "O4'" A UPV 4 ? ? 1.59 10 18 "HO2'" B G 15 ? ? "O4'" B C 16 ? ? 1.59 11 19 "HO2'" B G 15 ? ? "O4'" B C 16 ? ? 1.58 12 20 "HO2'" B U 13 ? ? "O4'" B A 14 ? ? 1.58 13 20 "HO2'" B G 15 ? ? "O4'" B C 16 ? ? 1.59 # 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 DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.60 108.30 2.30 0.30 N 2 1 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.56 108.30 2.26 0.30 N 3 1 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.15 122.90 -3.75 0.60 N 4 2 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.69 108.30 2.39 0.30 N 5 2 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.34 108.30 2.04 0.30 N 6 3 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.36 108.30 3.06 0.30 N 7 3 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.45 108.30 2.15 0.30 N 8 3 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.19 122.90 -3.71 0.60 N 9 4 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.55 108.30 2.25 0.30 N 10 4 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.11 122.90 -3.79 0.60 N 11 4 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.34 108.30 2.04 0.30 N 12 4 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.02 122.90 -3.88 0.60 N 13 5 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.36 108.30 3.06 0.30 N 14 5 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.38 108.30 2.08 0.30 N 15 6 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.48 108.30 3.18 0.30 N 16 6 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.39 108.30 2.09 0.30 N 17 6 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.25 122.90 -3.65 0.60 N 18 7 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.90 108.30 2.60 0.30 N 19 7 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.95 108.30 2.65 0.30 N 20 8 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.19 108.30 2.89 0.30 N 21 8 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.39 108.30 2.09 0.30 N 22 8 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.28 122.90 -3.62 0.60 N 23 9 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.39 108.30 3.09 0.30 N 24 9 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 111.15 108.30 2.85 0.30 N 25 9 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.71 122.90 -4.19 0.60 N 26 10 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.81 108.30 2.51 0.30 N 27 10 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 111.07 108.30 2.77 0.30 N 28 11 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.44 108.30 2.14 0.30 N 29 11 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 111.11 108.30 2.81 0.30 N 30 11 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.92 122.90 -3.98 0.60 N 31 12 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.91 108.30 2.61 0.30 N 32 12 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.20 122.90 -3.70 0.60 N 33 13 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.19 108.30 2.89 0.30 N 34 13 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.08 122.90 -3.82 0.60 N 35 13 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.76 108.30 2.46 0.30 N 36 14 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.96 108.30 2.66 0.30 N 37 14 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.67 108.30 2.37 0.30 N 38 14 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.90 122.90 -4.00 0.60 N 39 15 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.60 108.30 2.30 0.30 N 40 15 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.07 122.90 -3.83 0.60 N 41 15 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.21 108.30 1.91 0.30 N 42 15 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.99 122.90 -3.91 0.60 N 43 16 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.77 108.30 2.47 0.30 N 44 16 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.26 122.90 -3.64 0.60 N 45 16 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.79 108.30 2.49 0.30 N 46 16 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.15 122.90 -3.75 0.60 N 47 17 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.50 108.30 2.20 0.30 N 48 17 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.23 108.30 1.93 0.30 N 49 17 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.17 122.90 -3.73 0.60 N 50 18 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.88 108.30 2.58 0.30 N 51 18 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.92 108.30 2.62 0.30 N 52 19 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.63 108.30 2.33 0.30 N 53 19 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.56 108.30 2.26 0.30 N 54 20 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.88 108.30 2.58 0.30 N 55 20 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.89 108.30 2.59 0.30 N 56 20 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.04 122.90 -3.86 0.60 N # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id UPV _pdbx_struct_mod_residue.label_seq_id 4 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id UPV _pdbx_struct_mod_residue.auth_seq_id 4 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id U _pdbx_struct_mod_residue.details ? # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LVY _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 2LVY _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '0.9 mM duplex, 100% D2O' 1 '100% D2O' '0.9 mM duplex, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' # 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 duplex-1 0.9 ? mM ? 1 duplex-2 0.9 ? mM ? 2 # 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 0 6.7 ambient ? 293 K 2 0 6.7 ambient ? 283 K # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D DQF-COSY' 1 2 1 '2D 1H-31P HETCOR' 1 3 1 '2D 1H-1H NOESY' 2 4 2 '2D 1H-1H NOESY' # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2LVY _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count 14 _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count 14 _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count 14 _pdbx_nmr_constraints.NA_other-angle_constraints_total_count 14 _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count 32 _pdbx_nmr_constraints.NOE_constraints_total 292 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 145 _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 ? # _pdbx_nmr_refine.entry_id 2LVY _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' 'X-PLOR NIH' 2.25 1 'Schwieters, Kuszewski, Tjandra and Clore' refinement 'X-PLOR NIH' 2.25 2 # 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 DT OP3 O N N 73 DT P P N N 74 DT OP1 O N N 75 DT OP2 O N N 76 DT "O5'" O N N 77 DT "C5'" C N N 78 DT "C4'" C N R 79 DT "O4'" O N N 80 DT "C3'" C N S 81 DT "O3'" O N N 82 DT "C2'" C N N 83 DT "C1'" C N R 84 DT N1 N N N 85 DT C2 C N N 86 DT O2 O N N 87 DT N3 N N N 88 DT C4 C N N 89 DT O4 O N N 90 DT C5 C N N 91 DT C7 C N N 92 DT C6 C N N 93 DT HOP3 H N N 94 DT HOP2 H N N 95 DT "H5'" H N N 96 DT "H5''" H N N 97 DT "H4'" H N N 98 DT "H3'" H N N 99 DT "HO3'" H N N 100 DT "H2'" H N N 101 DT "H2''" H N N 102 DT "H1'" H N N 103 DT H3 H N N 104 DT H71 H N N 105 DT H72 H N N 106 DT H73 H N N 107 DT 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 UPV P P N N 181 UPV N1 N N N 182 UPV C2 C N N 183 UPV O2 O N N 184 UPV N3 N N N 185 UPV C4 C N N 186 UPV O4 O N N 187 UPV C5 C N N 188 UPV C6 C N N 189 UPV CA C N N 190 UPV CB C N N 191 UPV CG C N N 192 UPV "C1'" C N R 193 UPV "C2'" C N R 194 UPV "O2'" O N N 195 UPV "C3'" C N R 196 UPV "O3'" O N N 197 UPV "C4'" C N R 198 UPV "O4'" O N N 199 UPV "C5'" C N N 200 UPV "O5'" O N N 201 UPV OB1 O N N 202 UPV OB2 O N N 203 UPV CD1 C N N 204 UPV CD2 C N N 205 UPV CD3 C N N 206 UPV OP3 O N N 207 UPV OP2 O N N 208 UPV HN3 H N N 209 UPV H5 H N N 210 UPV H6 H N N 211 UPV "H5'" H N N 212 UPV "H1'" H N N 213 UPV HD1 H N N 214 UPV HD1A H N N 215 UPV HD1B H N N 216 UPV "H2'" H N N 217 UPV HD2 H N N 218 UPV HD2A H N N 219 UPV HD2B H N N 220 UPV "H3'" H N N 221 UPV HD3 H N N 222 UPV HD3A H N N 223 UPV HD3B H N N 224 UPV "H4'" H N N 225 UPV "H5'A" H N N 226 UPV HA H N N 227 UPV HAA H N N 228 UPV "HO3'" H N N 229 UPV HOP3 H N N 230 UPV HOP2 H N N 231 UPV OP1 O N N 232 # 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 DT OP3 P sing N N 76 DT OP3 HOP3 sing N N 77 DT P OP1 doub N N 78 DT P OP2 sing N N 79 DT P "O5'" sing N N 80 DT OP2 HOP2 sing N N 81 DT "O5'" "C5'" sing N N 82 DT "C5'" "C4'" sing N N 83 DT "C5'" "H5'" sing N N 84 DT "C5'" "H5''" sing N N 85 DT "C4'" "O4'" sing N N 86 DT "C4'" "C3'" sing N N 87 DT "C4'" "H4'" sing N N 88 DT "O4'" "C1'" sing N N 89 DT "C3'" "O3'" sing N N 90 DT "C3'" "C2'" sing N N 91 DT "C3'" "H3'" sing N N 92 DT "O3'" "HO3'" sing N N 93 DT "C2'" "C1'" sing N N 94 DT "C2'" "H2'" sing N N 95 DT "C2'" "H2''" sing N N 96 DT "C1'" N1 sing N N 97 DT "C1'" "H1'" sing N N 98 DT N1 C2 sing N N 99 DT N1 C6 sing N N 100 DT C2 O2 doub N N 101 DT C2 N3 sing N N 102 DT N3 C4 sing N N 103 DT N3 H3 sing N N 104 DT C4 O4 doub N N 105 DT C4 C5 sing N N 106 DT C5 C7 sing N N 107 DT C5 C6 doub N N 108 DT C7 H71 sing N N 109 DT C7 H72 sing N N 110 DT C7 H73 sing N N 111 DT 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 UPV P OP3 sing N N 188 UPV N1 C6 sing N N 189 UPV N1 "C1'" sing N N 190 UPV C2 N1 sing N N 191 UPV O2 C2 doub N N 192 UPV N3 C2 sing N N 193 UPV N3 C4 sing N N 194 UPV C4 C5 sing N N 195 UPV O4 C4 doub N N 196 UPV C5 H5 sing N N 197 UPV C5 C6 doub N N 198 UPV C6 H6 sing N N 199 UPV CA HAA sing N N 200 UPV CA "O2'" sing N N 201 UPV CB OB1 sing N N 202 UPV CB OB2 doub N N 203 UPV CG CB sing N N 204 UPV "C1'" "O4'" sing N N 205 UPV "C1'" "C2'" sing N N 206 UPV "C2'" "O2'" sing N N 207 UPV "C2'" "C3'" sing N N 208 UPV "C3'" "O3'" sing N N 209 UPV "O3'" "HO3'" sing N N 210 UPV "C4'" "C3'" sing N N 211 UPV "C4'" "C5'" sing N N 212 UPV "C4'" "H4'" sing N N 213 UPV "O4'" "C4'" sing N N 214 UPV "C5'" "H5'A" sing N N 215 UPV "O5'" P sing N N 216 UPV "O5'" "C5'" sing N N 217 UPV OB1 CA sing N N 218 UPV CD1 CG sing N N 219 UPV CD1 HD1B sing N N 220 UPV CD1 HD1A sing N N 221 UPV CD2 CG sing N N 222 UPV CD2 HD2B sing N N 223 UPV CD2 HD2 sing N N 224 UPV CD3 CG sing N N 225 UPV CD3 HD3 sing N N 226 UPV CD3 HD3B sing N N 227 UPV OP3 HOP3 sing N N 228 UPV OP2 P sing N N 229 UPV OP2 HOP2 sing N N 230 UPV HN3 N3 sing N N 231 UPV "H5'" "C5'" sing N N 232 UPV "H1'" "C1'" sing N N 233 UPV HD1 CD1 sing N N 234 UPV "H2'" "C2'" sing N N 235 UPV HD2A CD2 sing N N 236 UPV "H3'" "C3'" sing N N 237 UPV HD3A CD3 sing N N 238 UPV HA CA sing N N 239 UPV P OP1 doub N N 240 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LVY 'double helix' 2LVY '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 C 1 1_555 B G 8 1_555 1.197 -0.854 -1.349 1.860 15.409 -8.888 1 A_C1:G17_B A 1 ? B 17 ? 19 1 1 A G 2 1_555 B C 7 1_555 -0.393 -0.877 -2.082 -16.729 5.213 -13.288 2 A_G2:C16_B A 2 ? B 16 ? 19 1 1 A C 3 1_555 B G 6 1_555 0.266 -0.437 -0.624 -7.829 0.697 -3.174 3 A_C3:G15_B A 3 ? B 15 ? 19 1 1 A A 5 1_555 B U 4 1_555 0.061 -0.298 -0.520 3.857 -0.115 -1.705 4 A_A5:U13_B A 5 ? B 13 ? 20 1 1 A C 6 1_555 B G 3 1_555 1.118 -0.289 -0.857 26.147 -13.130 6.635 5 A_C6:G12_B A 6 ? B 12 ? 19 1 1 A G 7 1_555 B C 2 1_555 -0.634 -0.286 -1.430 -27.920 1.900 1.621 6 A_G7:C11_B A 7 ? B 11 ? 19 1 1 A C 8 1_555 B G 1 1_555 1.144 -0.516 -0.547 -1.760 18.379 -10.968 7 A_C8:G10_B A 8 ? B 10 ? 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 C 1 1_555 B G 8 1_555 A G 2 1_555 B C 7 1_555 -0.085 -1.285 5.160 4.152 -6.514 24.945 0.045 2.031 5.238 -14.638 -9.331 26.096 1 AA_C1G2:C16G17_BB A 1 ? B 17 ? A 2 ? B 16 ? 1 A G 2 1_555 B C 7 1_555 A C 3 1_555 B G 6 1_555 0.751 -1.492 3.541 -5.708 -9.687 36.505 -0.904 -1.961 3.652 -15.031 8.857 38.141 2 AA_G2C3:G15C16_BB A 2 ? B 16 ? A 3 ? B 15 ? 1 A C 3 1_555 B G 6 1_555 A A 5 1_555 B U 4 1_555 -0.279 -2.175 6.906 0.668 3.319 59.079 -2.557 0.354 6.783 3.363 -0.677 59.168 3 AA_C3A5:U13G15_BB A 3 ? B 15 ? A 5 ? B 13 ? 1 A A 5 1_555 B U 4 1_555 A C 6 1_555 B G 3 1_555 1.062 -1.177 2.912 1.755 -4.704 34.119 -1.312 -1.540 3.091 -7.963 -2.971 34.475 4 AA_A5C6:G12U13_BB A 5 ? B 13 ? A 6 ? B 12 ? 1 A C 6 1_555 B G 3 1_555 A G 7 1_555 B C 2 1_555 -0.317 -2.715 5.310 0.343 6.957 23.242 -9.774 0.917 4.320 16.791 -0.827 24.250 5 AA_C6G7:C11G12_BB A 6 ? B 12 ? A 7 ? B 11 ? 1 A G 7 1_555 B C 2 1_555 A C 8 1_555 B G 1 1_555 -1.619 -1.120 2.881 -3.101 -2.894 37.406 -1.394 2.142 3.076 -4.494 4.816 37.637 6 AA_G7C8:G10C11_BB A 7 ? B 11 ? A 8 ? B 10 ? # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 500 Bruker AVANCE 1 'Bruker Avance' 600 Bruker AVANCE 2 'Bruker Avance' # _atom_sites.entry_id 2LVY _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_