data_6430 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H and 31P chemical shift assignments for HIV-1 integrase inhibitor 93del ; _BMRB_accession_number 6430 _BMRB_flat_file_name bmr6430.str _Entry_type original _Submission_date 2004-12-13 _Accession_date 2004-12-13 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Phan 'Anh Tuan' . . 2 Kuryavyi Vitaly . . 3 Ma Jin-Biao . . 4 Faure Aurelie . . 5 Andreola Marie-Line . . 6 Patel Dinshaw J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 148 "31P chemical shifts" 15 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2009-07-06 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Phan 'Anh Tuan' . . 2 Kuryavyi Vitaly . . 3 Ma Jin-Biao . . 4 Faure Aurelie . . 5 Andreola Marie-Line . . 6 Patel Dinshaw J. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_volume 102 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 634 _Page_last 639 _Year 2005 _Details . loop_ _Keyword 'dimeric G-quadruplex' 'DNA aptamer' 'HIV-1 integrase' 'inhibitor design' stop_ save_ ################################## # Molecular system description # ################################## save_system_93del _Saveframe_category molecular_system _Mol_system_name 'HIV-1 integrase inhibitor, 93del' _Abbreviation_common 93del _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '93del subunit 1' $93del '93del subunit 2' $93del stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'HIV-1 integrase inhibitor' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_93del _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'HIV-1 integrase inhibitor' _Abbreviation_common 93del _Molecular_mass . _Mol_thiol_state 'not present' _Details ; 93del is a potent nanomolar inhibitor of HIV-1 integrase. This guanine-rich DNA sequence adopts an unusually stable dimeric quadruplex in K+ solution involving six continuously stacked G-tetrads. ; ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence GGGGTGGGAGGAGGGT loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DG 5 DT 6 DG 7 DG 8 DG 9 DA 10 DG 11 DG 12 DA 13 DG 14 DG 15 DG 16 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $93del . . unclassified . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $93del 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $93del 2.0 mM 1.5 2.5 . K+ 0.09 M . . . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $93del 9.0 mM 8.5 9.5 . K+ 0.09 M . . . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version . _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Unity INOVA' _Field_strength 500 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Unity INOVA' _Field_strength 600 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-15N_JRHMQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N JRHMQC' _Sample_label . save_ save_1H-15N_HMBC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N HMBC' _Sample_label . save_ save_1H-13C_JRHMBC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C JRHMBC' _Sample_label . save_ save_1H-13C_HMBC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HMBC' _Sample_label . save_ save_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HSQC' _Sample_label . save_ save_1H-13C_sHMBC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C sHMBC' _Sample_label . save_ save_1H-31P_TOCSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P TOCSY' _Sample_label . save_ save_1H-31P_HSQC_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P HSQC' _Sample_label . save_ save_1H-1H_COSY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H COSY' _Sample_label . save_ save_1H-1H_TOCSY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _Sample_label . save_ save_1H-1H_JRNOESY_11 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H JRNOESY' _Sample_label . save_ save_1H-1H_NOESY_12 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N JRHMQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N HMBC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C JRHMBC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HMBC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C sHMBC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_9 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_10 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_11 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H JRNOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_12 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 0.2 n/a temperature 298 2 K 'ionic strength' 90 . mM stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 DSS P 31 'methyl protons' ppm 0.0 . indirect . . . 0.404808636 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '93del subunit 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 DG H8 H 6.07 0.05 1 2 . 1 DG H1 H 11.39 0.05 1 3 . 1 DG H1' H 4.1 0.05 1 4 . 1 DG H2' H 2.04 0.05 1 5 . 1 DG H2'' H 2.7 0.05 1 6 . 1 DG H3' H 4.83 0.05 1 7 . 1 DG H4' H 4.3 0.05 1 8 . 1 DG H5' H 4.37 0.05 2 9 . 1 DG H5'' H 3.87 0.05 2 10 . 2 DG H8 H 7.81 0.05 1 11 . 2 DG H1 H 11.45 0.05 1 12 . 2 DG H1' H 5.84 0.05 1 13 . 2 DG H2' H 2.47 0.05 1 14 . 2 DG H2'' H 2.71 0.05 1 15 . 2 DG H3' H 5.07 0.05 1 16 . 2 DG H4' H 4.29 0.05 1 17 . 2 DG H5' H 4.3 0.05 2 18 . 2 DG H5'' H 3.4 0.05 2 19 . 2 DG P P -4.36 0.05 1 20 . 3 DG H8 H 7.68 0.05 1 21 . 3 DG H1 H 11.35 0.05 1 22 . 3 DG H1' H 6.19 0.05 1 23 . 3 DG H2' H 2.68 0.05 1 24 . 3 DG H2'' H 2.94 0.05 1 25 . 3 DG H3' H 5.03 0.05 1 26 . 3 DG H4' H 4.64 0.05 1 27 . 3 DG H5' H 4.38 0.05 2 28 . 3 DG H5'' H 4.39 0.05 2 29 . 3 DG P P -3.92 0.05 1 30 . 4 DG H8 H 7.82 0.05 1 31 . 4 DG H1 H 11.37 0.05 1 32 . 4 DG H1' H 6.42 0.05 1 33 . 4 DG H2' H 2.7 0.05 1 34 . 4 DG H2'' H 2.55 0.05 1 35 . 4 DG H3' H 5.12 0.05 1 36 . 4 DG H4' H 4.63 0.05 1 37 . 4 DG H5' H 4.27 0.05 2 38 . 4 DG H5'' H 4.36 0.05 2 39 . 4 DG P P -4.62 0.05 1 40 . 5 DT H6 H 7.88 0.05 1 41 . 5 DT H71 H 2.01 0.05 1 42 . 5 DT H72 H 2.01 0.05 1 43 . 5 DT H73 H 2.01 0.05 1 44 . 5 DT H1' H 6.56 0.05 1 45 . 5 DT H2' H 2.5 0.05 1 46 . 5 DT H2'' H 2.71 0.05 1 47 . 5 DT H3' H 5.08 0.05 1 48 . 5 DT H4' H 4.6 0.05 1 49 . 5 DT H5' H 4.26 0.05 2 50 . 5 DT H5'' H 4.36 0.05 2 51 . 5 DT P P -5.65 0.05 1 52 . 6 DG H8 H 7.61 0.05 1 53 . 6 DG H1 H 10.90 0.05 1 54 . 6 DG H1' H 6.03 0.05 1 55 . 6 DG H2' H 2.55 0.05 1 56 . 6 DG H2'' H 2.89 0.05 1 57 . 6 DG H3' H 4.95 0.05 1 58 . 6 DG H4' H 4.57 0.05 1 59 . 6 DG H5' H 4.35 0.05 2 60 . 6 DG H5'' H 4.4 0.05 2 61 . 6 DG P P -3.08 0.05 1 62 . 7 DG H8 H 7.92 0.05 1 63 . 7 DG H1 H 11.03 0.05 1 64 . 7 DG H1' H 6.27 0.05 1 65 . 7 DG H2' H 2.75 0.05 1 66 . 7 DG H2'' H 2.92 0.05 1 67 . 7 DG H3' H 5.1 0.05 1 68 . 7 DG H4' H 4.71 0.05 1 69 . 7 DG H5' H 4.35 0.05 2 70 . 7 DG H5'' H 4.37 0.05 2 71 . 7 DG P P -4.04 0.05 1 72 . 8 DG H8 H 7.55 0.05 1 73 . 8 DG H1 H 11.32 0.05 1 74 . 8 DG H1' H 6.17 0.05 1 75 . 8 DG H2' H 2.3 0.05 1 76 . 8 DG H2'' H 2.3 0.05 1 77 . 8 DG H3' H 4.74 0.05 1 78 . 8 DG H4' H 3.01 0.05 1 79 . 8 DG H5' H 3.79 0.05 2 80 . 8 DG H5'' H 3.8 0.05 2 81 . 8 DG P P -4.74 0.05 1 82 . 9 DA H8 H 9.1 0.05 1 83 . 9 DA H2 H 8.5 0.05 1 84 . 9 DA H1' H 6.66 0.05 1 85 . 9 DA H2' H 3.19 0.05 1 86 . 9 DA H2'' H 3.32 0.05 1 87 . 9 DA H3' H 5.53 0.05 1 88 . 9 DA H4' H 4.41 0.05 1 89 . 9 DA H5' H 3.98 0.05 2 90 . 9 DA H5'' H 4.17 0.05 2 91 . 9 DA P P -2.96 0.05 1 92 . 10 DG H8 H 7.77 0.05 1 93 . 10 DG H1 H 10.93 0.05 1 94 . 10 DG H1' H 6.16 0.05 1 95 . 10 DG H2' H 2.49 0.05 1 96 . 10 DG H2'' H 2.81 0.05 1 97 . 10 DG H3' H 4.99 0.05 1 98 . 10 DG H4' H 4.43 0.05 1 99 . 10 DG H5' H 4.37 0.05 2 100 . 10 DG H5'' H 3.87 0.05 2 101 . 10 DG P P -3.15 0.05 1 102 . 11 DG H8 H 8.04 0.05 1 103 . 11 DG H1 H 10.92 0.05 1 104 . 11 DG H1' H 6.48 0.05 1 105 . 11 DG H2' H 2.72 0.05 1 106 . 11 DG H2'' H 2.51 0.05 1 107 . 11 DG H3' H 5.07 0.05 1 108 . 11 DG H4' H 4.67 0.05 1 109 . 11 DG H5' H 4.23 0.05 2 110 . 11 DG H5'' H 4.34 0.05 2 111 . 11 DG P P -4.51 0.05 1 112 . 12 DA H8 H 8.53 0.05 1 113 . 12 DA H2 H 8.33 0.05 1 114 . 12 DA H1' H 6.69 0.05 1 115 . 12 DA H2' H 2.92 0.05 1 116 . 12 DA H2'' H 2.92 0.05 1 117 . 12 DA H3' H 5.16 0.05 1 118 . 12 DA H4' H 4.76 0.05 1 119 . 12 DA H5' H 4.23 0.05 2 120 . 12 DA H5'' H 4.31 0.05 2 121 . 12 DA P P -5.43 0.05 1 122 . 13 DG H8 H 7.56 0.05 1 123 . 13 DG H1 H 10.91 0.05 1 124 . 13 DG H1' H 5.93 0.05 1 125 . 13 DG H2' H 2.39 0.05 1 126 . 13 DG H2'' H 2.76 0.05 1 127 . 13 DG H3' H 5 0.05 1 128 . 13 DG H4' H 4.5 0.05 1 129 . 13 DG H5' H 4.3 0.05 2 130 . 13 DG H5'' H 4.41 0.05 2 131 . 13 DG P P -2.72 0.05 1 132 . 14 DG H8 H 7.96 0.05 1 133 . 14 DG H1 H 11.07 0.05 1 134 . 14 DG H1' H 6.05 0.05 1 135 . 14 DG H2' H 2.7 0.05 1 136 . 14 DG H2'' H 2.78 0.05 1 137 . 14 DG H3' H 5.09 0.05 1 138 . 14 DG H4' H 4.53 0.05 1 139 . 14 DG H5' H 4.22 0.05 2 140 . 14 DG H5'' H 4.3 0.05 2 141 . 14 DG P P -3.89 0.05 1 142 . 15 DG H8 H 7.72 0.05 1 143 . 15 DG H1 H 11.14 0.05 1 144 . 15 DG H1' H 6.22 0.05 1 145 . 15 DG H2' H 2.59 0.05 1 146 . 15 DG H2'' H 2.81 0.05 1 147 . 15 DG H3' H 4.99 0.05 1 148 . 15 DG H4' H 4.53 0.05 1 149 . 15 DG H5' H 4.18 0.05 2 150 . 15 DG H5'' H 4.34 0.05 2 151 . 15 DG P P -4.21 0.05 1 152 . 16 DT H6 H 7.2 0.05 1 153 . 16 DT H71 H 1.53 0.05 1 154 . 16 DT H72 H 1.53 0.05 1 155 . 16 DT H73 H 1.53 0.05 1 156 . 16 DT H1' H 5.97 0.05 1 157 . 16 DT H2' H 2.13 0.05 1 158 . 16 DT H2'' H 2.13 0.05 1 159 . 16 DT H3' H 4.47 0.05 1 160 . 16 DT H4' H 4.01 0.05 1 161 . 16 DT H5' H 4.09 0.05 2 162 . 16 DT H5'' H 4.25 0.05 2 163 . 16 DT P P -4.16 0.05 1 stop_ save_