data_1AUL # _entry.id 1AUL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1AUL pdb_00001aul 10.2210/pdb1aul/pdb WWPDB D_1000171277 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1AUL _pdbx_database_status.recvd_initial_deposition_date 1997-08-29 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Kumar, S.' 1 'Reed, M.W.' 2 'Gamper Junior, H.B.' 3 'Gorn, V.V.' 4 'Lukhtanov, E.A.' 5 'Foti, M.' 6 'West, J.' 7 'Meyer Junior, R.B.' 8 'Schweitzer, B.I.' 9 # _citation.id primary _citation.title 'Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 26 _citation.page_first 831 _citation.page_last 838 _citation.year 1998 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9443977 _citation.pdbx_database_id_DOI 10.1093/nar/26.3.831 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kumar, S.' 1 ? primary 'Reed, M.W.' 2 ? primary 'Gamper Jr., H.B.' 3 ? primary 'Gorn, V.V.' 4 ? primary 'Lukhtanov, E.A.' 5 ? primary 'Foti, M.' 6 ? primary 'West, J.' 7 ? primary 'Meyer Jr., R.B.' 8 ? primary 'Schweitzer, B.I.' 9 ? # _cell.entry_id 1AUL _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AUL _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # 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 ;DNA (5'-D(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3') ; 3744.794 1 ? ? ? 'TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA RESIDUE WITH A HEXAMETHYLENE LINKER' 2 polymer syn ;DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3') ; 3037.032 1 ? ? ? 'TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA RESIDUE WITH A HEXAMETHYLENE LINKER' # 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 polydeoxyribonucleotide no yes '(THX)(DG)(DA)(DT)(DT)(DA)(DT)(DC)(DT)(DG)' NGATTATCTG A ? 2 polydeoxyribonucleotide no no '(DC)(DA)(DG)(DA)(DT)(DA)(DA)(DT)(DC)(DA)' CAGATAATCA B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 THX n 1 2 DG n 1 3 DA n 1 4 DT n 1 5 DT n 1 6 DA n 1 7 DT n 1 8 DC n 1 9 DT n 1 10 DG n 2 1 DC n 2 2 DA n 2 3 DG n 2 4 DA n 2 5 DT n 2 6 DA n 2 7 DA n 2 8 DT n 2 9 DC n 2 10 DA n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? ;CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER ; 2 1 sample ? ? ? ? ? ;CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER ; # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1AUL 1AUL ? ? ? 2 2 PDB 1AUL 1AUL ? ? ? # 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 1AUL A 1 ? 10 ? 1AUL 1 ? 10 ? 1 10 2 2 1AUL B 1 ? 10 ? 1AUL 11 ? 20 ? 11 20 # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 THX 'DNA linking' . ;PHOSPHONIC ACID 6-({6-[6-(6-CARBAMOYL-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONYL)-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDOCENE-2-CA RBONYL]-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONL}-AMINO)-HEXYL ESTER 5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL ESTER ; CDPI3 'C50 H53 N10 O12 P' 1016.989 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 DQF-COSY 1 3 1 HETEROTOCSY 1 4 1 TOCSY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 293.15 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model UNITYPLUS _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1AUL _pdbx_nmr_refine.method 'RESTRAINED MOLECULAR DYNAMICS/RELAXATION MATRIX REFINEMENT' _pdbx_nmr_refine.details ;CANONICAL B-TYPE STRUCTURE USED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS GENERATING SIX STRUCTURES FROM DIFFERENT RANDOM NUMBER SEEDS. THE SIX STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX REFINEMENT TO GENERATE THE SIX FINAL STRUCTURES. THESE SIX STRUCTURES WERE AVERAGED AND MINIMIZED TO GIVE THE FINAL STRUCTURE PRESENTED HERE. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1AUL _pdbx_nmr_ensemble.conformers_calculated_total_number 6 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'LEAST RESTRAINT VIOLATION' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR ? BRUNGER 1 'structure solution' X-PLOR 3.1 ? 2 # _exptl.entry_id 1AUL _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1AUL _struct.title 'SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1AUL _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DEOXYRIBONUCLEIC ACID, CDPI3, DNA' # 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 ? # _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 one ? A THX 1 "O3'" ? ? ? 1_555 A DG 2 P ? ? A THX 1 A DG 2 1_555 ? ? ? ? ? ? ? 1.734 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 2 B DC 19 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog2 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 4 B DA 16 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog5 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 7 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 7 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 9 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 9 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1AUL _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 # _atom_sites.entry_id 1AUL _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 THX 1 1 1 THX THX A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DG 10 10 10 DG G A . n B 2 1 DC 1 11 11 DC C B . n B 2 2 DA 2 12 12 DA A B . n B 2 3 DG 3 13 13 DG G B . n B 2 4 DA 4 14 14 DA A B . n B 2 5 DT 5 15 15 DT T B . n B 2 6 DA 6 16 16 DA A B . n B 2 7 DA 7 17 17 DA A B . n B 2 8 DT 8 18 18 DT T B . n B 2 9 DC 9 19 19 DC C B . n B 2 10 DA 10 20 20 DA A B . n # _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 # 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 1997-12-24 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 # _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' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' Other 6 4 'Structure model' 'Structure summary' # 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' chem_comp 2 4 'Structure model' database_2 3 4 'Structure model' pdbx_database_status 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 4 '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' '_chem_comp.name' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_pdbx_database_status.process_site' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 3 # 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 O4 A THX 1 ? ? H61 B DA 20 ? ? 1.39 2 1 H3 A THX 1 ? ? N1 B DA 20 ? ? 1.57 # 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 "O3'" A THX 1 ? ? P A DG 2 ? ? 1.734 1.607 0.127 0.012 Y 2 1 P A DG 2 ? ? "O5'" A DG 2 ? ? 1.742 1.593 0.149 0.010 N 3 1 "O3'" A DG 2 ? ? P A DA 3 ? ? 1.730 1.607 0.123 0.012 Y 4 1 P A DA 3 ? ? "O5'" A DA 3 ? ? 1.726 1.593 0.133 0.010 N 5 1 N9 A DA 3 ? ? C4 A DA 3 ? ? 1.332 1.374 -0.042 0.006 N 6 1 "O3'" A DA 3 ? ? P A DT 4 ? ? 1.731 1.607 0.124 0.012 Y 7 1 P A DT 4 ? ? "O5'" A DT 4 ? ? 1.733 1.593 0.140 0.010 N 8 1 "O3'" A DT 4 ? ? P A DT 5 ? ? 1.725 1.607 0.118 0.012 Y 9 1 P A DT 5 ? ? "O5'" A DT 5 ? ? 1.716 1.593 0.123 0.010 N 10 1 "O3'" A DT 5 ? ? P A DA 6 ? ? 1.722 1.607 0.115 0.012 Y 11 1 P A DA 6 ? ? "O5'" A DA 6 ? ? 1.727 1.593 0.134 0.010 N 12 1 "C3'" A DA 6 ? ? "C2'" A DA 6 ? ? 1.652 1.518 0.134 0.012 N 13 1 "O3'" A DA 6 ? ? P A DT 7 ? ? 1.729 1.607 0.122 0.012 Y 14 1 P A DT 7 ? ? "O5'" A DT 7 ? ? 1.730 1.593 0.137 0.010 N 15 1 "O3'" A DT 7 ? ? P A DC 8 ? ? 1.734 1.607 0.127 0.012 Y 16 1 P A DC 8 ? ? "O5'" A DC 8 ? ? 1.733 1.593 0.140 0.010 N 17 1 "O3'" A DC 8 ? ? P A DT 9 ? ? 1.730 1.607 0.123 0.012 Y 18 1 P A DT 9 ? ? "O5'" A DT 9 ? ? 1.726 1.593 0.133 0.010 N 19 1 "C2'" A DT 9 ? ? "C1'" A DT 9 ? ? 1.589 1.519 0.070 0.010 N 20 1 "O3'" A DT 9 ? ? P A DG 10 ? ? 1.732 1.607 0.125 0.012 Y 21 1 P A DG 10 ? ? "O5'" A DG 10 ? ? 1.732 1.593 0.139 0.010 N 22 1 "C2'" B DC 11 ? ? "C1'" B DC 11 ? ? 1.584 1.519 0.065 0.010 N 23 1 "O3'" B DC 11 ? ? P B DA 12 ? ? 1.737 1.607 0.130 0.012 Y 24 1 P B DA 12 ? ? "O5'" B DA 12 ? ? 1.733 1.593 0.140 0.010 N 25 1 "O3'" B DA 12 ? ? P B DG 13 ? ? 1.726 1.607 0.119 0.012 Y 26 1 P B DG 13 ? ? "O5'" B DG 13 ? ? 1.727 1.593 0.134 0.010 N 27 1 "O3'" B DG 13 ? ? P B DA 14 ? ? 1.728 1.607 0.121 0.012 Y 28 1 P B DA 14 ? ? "O5'" B DA 14 ? ? 1.726 1.593 0.133 0.010 N 29 1 "O3'" B DA 14 ? ? P B DT 15 ? ? 1.731 1.607 0.124 0.012 Y 30 1 P B DT 15 ? ? "O5'" B DT 15 ? ? 1.736 1.593 0.143 0.010 N 31 1 "O3'" B DT 15 ? ? P B DA 16 ? ? 1.728 1.607 0.121 0.012 Y 32 1 P B DA 16 ? ? "O5'" B DA 16 ? ? 1.730 1.593 0.137 0.010 N 33 1 "C2'" B DA 16 ? ? "C1'" B DA 16 ? ? 1.581 1.519 0.062 0.010 N 34 1 "O3'" B DA 16 ? ? P B DA 17 ? ? 1.723 1.607 0.116 0.012 Y 35 1 P B DA 17 ? ? "O5'" B DA 17 ? ? 1.718 1.593 0.125 0.010 N 36 1 "O3'" B DA 17 ? ? P B DT 18 ? ? 1.724 1.607 0.117 0.012 Y 37 1 P B DT 18 ? ? "O5'" B DT 18 ? ? 1.744 1.593 0.151 0.010 N 38 1 "O3'" B DT 18 ? ? P B DC 19 ? ? 1.752 1.607 0.145 0.012 Y 39 1 P B DC 19 ? ? "O5'" B DC 19 ? ? 1.738 1.593 0.145 0.010 N 40 1 "C2'" B DC 19 ? ? "C1'" B DC 19 ? ? 1.601 1.519 0.082 0.010 N 41 1 "O3'" B DC 19 ? ? P B DA 20 ? ? 1.736 1.607 0.129 0.012 Y 42 1 P B DA 20 ? ? "O5'" B DA 20 ? ? 1.726 1.593 0.133 0.010 N 43 1 "C3'" B DA 20 ? ? "C2'" B DA 20 ? ? 1.593 1.518 0.075 0.012 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 C5 A DG 10 ? ? C6 A DG 10 ? ? O6 A DG 10 ? ? 124.88 128.60 -3.72 0.60 N 2 1 C5 B DG 13 ? ? C6 B DG 13 ? ? O6 B DG 13 ? ? 124.88 128.60 -3.72 0.60 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 DC B 19 ? ? 0.072 'SIDE CHAIN' 2 1 DA B 20 ? ? 0.059 'SIDE CHAIN' # _pdbx_validate_polymer_linkage.id 1 _pdbx_validate_polymer_linkage.PDB_model_num 1 _pdbx_validate_polymer_linkage.auth_atom_id_1 "O3'" _pdbx_validate_polymer_linkage.auth_asym_id_1 B _pdbx_validate_polymer_linkage.auth_comp_id_1 DT _pdbx_validate_polymer_linkage.auth_seq_id_1 18 _pdbx_validate_polymer_linkage.PDB_ins_code_1 ? _pdbx_validate_polymer_linkage.label_alt_id_1 ? _pdbx_validate_polymer_linkage.auth_atom_id_2 P _pdbx_validate_polymer_linkage.auth_asym_id_2 B _pdbx_validate_polymer_linkage.auth_comp_id_2 DC _pdbx_validate_polymer_linkage.auth_seq_id_2 19 _pdbx_validate_polymer_linkage.PDB_ins_code_2 ? _pdbx_validate_polymer_linkage.label_alt_id_2 ? _pdbx_validate_polymer_linkage.dist 1.75 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1AUL 'double helix' 1AUL 'b-form double helix' # 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 DG 2 1_555 B DC 9 1_555 0.840 0.149 0.941 0.709 7.219 26.294 1 A_DG2:DC19_B A 2 ? B 19 ? ? 1 1 A DA 3 1_555 B DT 8 1_555 -1.088 -0.539 0.744 3.244 -20.653 14.693 2 A_DA3:DT18_B A 3 ? B 18 ? 20 1 1 A DT 4 1_555 B DA 7 1_555 0.144 -0.460 1.258 -24.666 -11.516 14.899 3 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DT 5 1_555 B DA 6 1_555 -0.283 -0.212 0.534 -9.415 -1.416 4.457 4 A_DT5:DA16_B A 5 ? B 16 ? 20 1 1 A DA 6 1_555 B DT 5 1_555 0.467 -0.077 -0.465 -1.083 -6.569 -6.322 5 A_DA6:DT15_B A 6 ? B 15 ? 20 1 1 A DT 7 1_555 B DA 4 1_555 -0.175 -0.122 -0.590 16.877 -14.113 1.194 6 A_DT7:DA14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.684 -0.242 -0.424 7.590 -8.338 3.882 7 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DT 9 1_555 B DA 2 1_555 0.400 -0.259 0.176 9.588 -7.991 -5.710 8 A_DT9:DA12_B A 9 ? B 12 ? 20 1 1 A DG 10 1_555 B DC 1 1_555 -0.616 -0.342 0.206 6.923 1.045 -3.536 9 A_DG10:DC11_B A 10 ? B 11 ? 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 DG 2 1_555 B DC 9 1_555 A DA 3 1_555 B DT 8 1_555 0.023 -0.895 3.171 9.932 7.125 26.185 -3.287 2.032 2.674 14.748 -20.557 28.852 1 AA_DG2DA3:DT18DC19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DA 3 1_555 B DT 8 1_555 A DT 4 1_555 B DA 7 1_555 0.458 -0.197 4.347 -0.655 9.642 41.736 -1.545 -0.715 4.196 13.320 0.905 42.791 2 AA_DA3DT4:DA17DT18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DT 5 1_555 B DA 6 1_555 -0.064 -0.560 3.031 3.245 3.791 29.174 -1.830 0.755 2.913 7.458 -6.383 29.589 3 AA_DT4DT5:DA16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DT 5 1_555 B DA 6 1_555 A DA 6 1_555 B DT 5 1_555 -0.531 -1.104 2.762 10.725 6.010 33.881 -2.467 2.074 2.273 9.916 -17.696 35.981 4 AA_DT5DA6:DT15DA16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DA 6 1_555 B DT 5 1_555 A DT 7 1_555 B DA 4 1_555 0.506 -0.384 2.782 -0.186 6.151 34.183 -1.435 -0.871 2.672 10.360 0.313 34.716 5 AA_DA6DT7:DA14DT15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DT 7 1_555 B DA 4 1_555 A DC 8 1_555 B DG 3 1_555 -0.478 -0.453 3.388 0.019 11.535 37.015 -2.124 0.723 3.115 17.651 -0.029 38.710 6 AA_DT7DC8:DG13DA14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DT 9 1_555 B DA 2 1_555 -0.102 -0.869 3.505 -4.169 -5.778 36.846 -0.524 -0.439 3.586 -9.038 6.521 37.505 7 AA_DC8DT9:DA12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DT 9 1_555 B DA 2 1_555 A DG 10 1_555 B DC 1 1_555 -0.705 -1.955 2.927 -10.600 2.490 28.346 -4.194 -0.595 2.824 4.864 20.704 30.325 8 AA_DT9DG10:DC11DA12_BB A 9 ? B 12 ? A 10 ? B 11 ? #