data_1P96 # _entry.id 1P96 # _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 1P96 pdb_00001p96 10.2210/pdb1p96/pdb RCSB RCSB019164 ? ? WWPDB D_1000019164 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1KVH _pdbx_database_related.details 'The complexed structure of the bulge DNA and natural product with a similar aglycone structure.' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1P96 _pdbx_database_status.recvd_initial_deposition_date 2003-05-09 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 'Hwang, G.S.' 1 'Jones, G.B.' 2 'Goldberg, I.H.' 3 # _citation.id primary _citation.title 'Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA' _citation.journal_abbrev Biochemistry _citation.journal_volume 42 _citation.page_first 8472 _citation.page_last 8483 _citation.year 2003 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12859193 _citation.pdbx_database_id_DOI 10.1021/bi030072d # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hwang, G.S.' 1 ? primary 'Jones, G.B.' 2 ? primary 'Goldberg, I.H.' 3 ? # 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 "5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3'" 4265.780 1 ? ? ? ? 2 polymer syn "5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3'" 3694.402 1 ? ? ? ? 3 non-polymer syn ;SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI) ; 529.580 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 polydeoxyribonucleotide no no '(DC)(DA)(DC)(DG)(DC)(DA)(DG)(DT)(DT)(DC)(DG)(DG)(DA)(DC)' CACGCAGTTCGGAC A ? 2 polydeoxyribonucleotide no no '(DG)(DT)(DC)(DC)(DG)(DA)(DT)(DG)(DC)(DG)(DT)(DG)' GTCCGATGCGTG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DA n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 DA n 1 7 DG n 1 8 DT n 1 9 DT n 1 10 DC n 1 11 DG n 1 12 DG n 1 13 DA n 1 14 DC n 2 1 DG n 2 2 DT n 2 3 DC n 2 4 DC n 2 5 DG n 2 6 DA n 2 7 DT n 2 8 DG n 2 9 DC n 2 10 DG n 2 11 DT n 2 12 DG 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 ? ? ? ? ? 'This sequence was synthesized by DNA synthesizer.' 2 1 sample ? ? ? ? ? 'This sequence was synthesized by DNA synthesizer.' # 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 1P96 1P96 ? ? ? 2 2 PDB 1P96 1P96 ? ? ? # 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 1P96 A 1 ? 14 ? 1P96 1 ? 14 ? 1 14 2 2 1P96 B 1 ? 12 ? 1P96 1 ? 12 ? 1 12 # 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 DDI non-polymer . ;SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI) ; ? 'C31 H31 N O7' 529.580 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 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 '2D TOCSY' 3 1 1 DQF-COSY 4 1 1 'H-P COSY' 5 1 1 COSY-45 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 6.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength '0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20' _pdbx_nmr_sample_details.solvent_system '90% H20/10% D20; 99.96% D20' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Bruker AVANCE 600 2 ? Varian INOVA 750 3 ? Varian INOVA 500 # _pdbx_nmr_refine.entry_id 1P96 _pdbx_nmr_refine.method ;distance geometry sinulated annealing ; _pdbx_nmr_refine.details 'The structures are based on a total of 694 NOE restranints and 166 dihedral angle restraints.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1P96 _pdbx_nmr_details.text 'This structure was determined using 2D homonuclear and heteronuclear techniques.' # _pdbx_nmr_ensemble.entry_id 1P96 _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'all calculated structures submitted' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1P96 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'all calculated structures submited have the least restraint violation and the lowst energy.' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal NMRPipe 2002.044.17.08 processing 'Delaglio, F.' 1 Sparky 3.106 'data analysis' 'Goddard, T.D. and Kneller, D.G.' 2 CNS 1.0 refinement 'Brunger, A.T. et al' 3 # _exptl.entry_id 1P96 _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.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _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 # _struct.entry_id 1P96 _struct.title 'Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1P96 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Wedge-shaped synthetic drug-bulged DNA complex, 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 ? C N N 3 ? # _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 hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 11 N3 ? ? A DA 2 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 11 O4 ? ? A DA 2 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 8 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 8 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 8 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog16 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 9 B DA 6 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog17 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DA 13 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 13 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DA 13 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 13 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 14 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 14 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 14 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 14 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 14 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 14 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A DDI 21 ? 4 'BINDING SITE FOR RESIDUE DDI A 21' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 4 DG A 7 ? DG A 7 . ? 1_555 ? 3 AC1 4 DT A 9 ? DT A 9 . ? 1_555 ? 4 AC1 4 DT B 7 ? DT B 7 . ? 1_555 ? # _database_PDB_matrix.entry_id 1P96 _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 1P96 _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 DC 1 1 1 DC CYT A . n A 1 2 DA 2 2 2 DA ADE A . n A 1 3 DC 3 3 3 DC CYT A . n A 1 4 DG 4 4 4 DG GUA A . n A 1 5 DC 5 5 5 DC CYT A . n A 1 6 DA 6 6 6 DA ADE A . n A 1 7 DG 7 7 7 DG GUA A . n A 1 8 DT 8 8 8 DT THY A . n A 1 9 DT 9 9 9 DT THY A . n A 1 10 DC 10 10 10 DC CYT A . n A 1 11 DG 11 11 11 DG GUA A . n A 1 12 DG 12 12 12 DG GUA A . n A 1 13 DA 13 13 13 DA ADE A . n A 1 14 DC 14 14 14 DC CYT A . n B 2 1 DG 1 1 1 DG GUA B . n B 2 2 DT 2 2 2 DT THY B . n B 2 3 DC 3 3 3 DC CYT B . n B 2 4 DC 4 4 4 DC CYT B . n B 2 5 DG 5 5 5 DG GUA B . n B 2 6 DA 6 6 6 DA ADE B . n B 2 7 DT 7 7 7 DT THY B . n B 2 8 DG 8 8 8 DG GUA B . n B 2 9 DC 9 9 9 DC CYT B . n B 2 10 DG 10 10 10 DG GUA B . n B 2 11 DT 11 11 11 DT THY B . n B 2 12 DG 12 12 12 DG GUA B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id DDI _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 21 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id DDI _pdbx_nonpoly_scheme.auth_mon_id DDI _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _struct_site_keywords.site_id 1 _struct_site_keywords.text INTERCALATION # _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,C # _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 2003-08-26 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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' database_2 2 4 'Structure model' pdbx_nmr_spectrometer 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 4 'Structure model' struct_site # 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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_spectrometer.model' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 C27 ? A DDI 21 ? 'WRONG HAND' . 2 1 C28 ? A DDI 21 ? 'WRONG HAND' . 3 1 C29 ? A DDI 21 ? 'WRONG HAND' . 4 1 C30 ? A DDI 21 ? 'WRONG HAND' . 5 1 C26 ? A DDI 21 ? 'WRONG HAND' . 6 1 C25 ? A DDI 21 ? 'WRONG HAND' . 7 1 C12 ? A DDI 21 ? 'WRONG HAND' . 8 1 C11 ? A DDI 21 ? 'WRONG HAND' . 9 1 C9 ? A DDI 21 ? 'WRONG HAND' . 10 2 C27 ? A DDI 21 ? 'WRONG HAND' . 11 2 C28 ? A DDI 21 ? 'WRONG HAND' . 12 2 C29 ? A DDI 21 ? 'WRONG HAND' . 13 2 C30 ? A DDI 21 ? 'WRONG HAND' . 14 2 C26 ? A DDI 21 ? 'WRONG HAND' . 15 2 C25 ? A DDI 21 ? 'WRONG HAND' . 16 2 C12 ? A DDI 21 ? 'WRONG HAND' . 17 2 C11 ? A DDI 21 ? 'WRONG HAND' . 18 2 C9 ? A DDI 21 ? 'WRONG HAND' . 19 3 C27 ? A DDI 21 ? 'WRONG HAND' . 20 3 C28 ? A DDI 21 ? 'WRONG HAND' . 21 3 C29 ? A DDI 21 ? 'WRONG HAND' . 22 3 C30 ? A DDI 21 ? 'WRONG HAND' . 23 3 C26 ? A DDI 21 ? 'WRONG HAND' . 24 3 C25 ? A DDI 21 ? 'WRONG HAND' . 25 3 C12 ? A DDI 21 ? 'WRONG HAND' . 26 3 C11 ? A DDI 21 ? 'WRONG HAND' . 27 3 C9 ? A DDI 21 ? 'WRONG HAND' . 28 4 C27 ? A DDI 21 ? 'WRONG HAND' . 29 4 C28 ? A DDI 21 ? 'WRONG HAND' . 30 4 C29 ? A DDI 21 ? 'WRONG HAND' . 31 4 C30 ? A DDI 21 ? 'WRONG HAND' . 32 4 C26 ? A DDI 21 ? 'WRONG HAND' . 33 4 C25 ? A DDI 21 ? 'WRONG HAND' . 34 4 C12 ? A DDI 21 ? 'WRONG HAND' . 35 4 C11 ? A DDI 21 ? 'WRONG HAND' . 36 4 C9 ? A DDI 21 ? 'WRONG HAND' . 37 5 C27 ? A DDI 21 ? 'WRONG HAND' . 38 5 C28 ? A DDI 21 ? 'WRONG HAND' . 39 5 C29 ? A DDI 21 ? 'WRONG HAND' . 40 5 C30 ? A DDI 21 ? 'WRONG HAND' . 41 5 C26 ? A DDI 21 ? 'WRONG HAND' . 42 5 C25 ? A DDI 21 ? 'WRONG HAND' . 43 5 C12 ? A DDI 21 ? 'WRONG HAND' . 44 5 C11 ? A DDI 21 ? 'WRONG HAND' . 45 5 C9 ? A DDI 21 ? 'WRONG HAND' . 46 6 C27 ? A DDI 21 ? 'WRONG HAND' . 47 6 C28 ? A DDI 21 ? 'WRONG HAND' . 48 6 C29 ? A DDI 21 ? 'WRONG HAND' . 49 6 C30 ? A DDI 21 ? 'WRONG HAND' . 50 6 C26 ? A DDI 21 ? 'WRONG HAND' . 51 6 C25 ? A DDI 21 ? 'WRONG HAND' . 52 6 C12 ? A DDI 21 ? 'WRONG HAND' . 53 6 C11 ? A DDI 21 ? 'WRONG HAND' . 54 6 C9 ? A DDI 21 ? 'WRONG HAND' . 55 7 C27 ? A DDI 21 ? 'WRONG HAND' . 56 7 C28 ? A DDI 21 ? 'WRONG HAND' . 57 7 C29 ? A DDI 21 ? 'WRONG HAND' . 58 7 C30 ? A DDI 21 ? 'WRONG HAND' . 59 7 C26 ? A DDI 21 ? 'WRONG HAND' . 60 7 C25 ? A DDI 21 ? 'WRONG HAND' . 61 7 C12 ? A DDI 21 ? 'WRONG HAND' . 62 7 C11 ? A DDI 21 ? 'WRONG HAND' . 63 7 C9 ? A DDI 21 ? 'WRONG HAND' . 64 8 C27 ? A DDI 21 ? 'WRONG HAND' . 65 8 C28 ? A DDI 21 ? 'WRONG HAND' . 66 8 C29 ? A DDI 21 ? 'WRONG HAND' . 67 8 C30 ? A DDI 21 ? 'WRONG HAND' . 68 8 C26 ? A DDI 21 ? 'WRONG HAND' . 69 8 C25 ? A DDI 21 ? 'WRONG HAND' . 70 8 C12 ? A DDI 21 ? 'WRONG HAND' . 71 8 C11 ? A DDI 21 ? 'WRONG HAND' . 72 8 C9 ? A DDI 21 ? 'WRONG HAND' . 73 9 C27 ? A DDI 21 ? 'WRONG HAND' . 74 9 C28 ? A DDI 21 ? 'WRONG HAND' . 75 9 C29 ? A DDI 21 ? 'WRONG HAND' . 76 9 C30 ? A DDI 21 ? 'WRONG HAND' . 77 9 C26 ? A DDI 21 ? 'WRONG HAND' . 78 9 C25 ? A DDI 21 ? 'WRONG HAND' . 79 9 C12 ? A DDI 21 ? 'WRONG HAND' . 80 9 C11 ? A DDI 21 ? 'WRONG HAND' . 81 9 C9 ? A DDI 21 ? 'WRONG HAND' . 82 10 C27 ? A DDI 21 ? 'WRONG HAND' . 83 10 C28 ? A DDI 21 ? 'WRONG HAND' . 84 10 C29 ? A DDI 21 ? 'WRONG HAND' . 85 10 C30 ? A DDI 21 ? 'WRONG HAND' . 86 10 C26 ? A DDI 21 ? 'WRONG HAND' . 87 10 C25 ? A DDI 21 ? 'WRONG HAND' . 88 10 C12 ? A DDI 21 ? 'WRONG HAND' . 89 10 C11 ? A DDI 21 ? 'WRONG HAND' . 90 10 C9 ? A DDI 21 ? 'WRONG HAND' . # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1P96 'double helix' 1P96 'bulge loop' # 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 DC 1 1_555 B DG 12 1_555 0.274 -0.043 0.713 -4.621 18.115 2.782 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DA 2 1_555 B DT 11 1_555 -0.185 -0.293 1.407 21.060 15.436 0.902 2 A_DA2:DT11_B A 2 ? B 11 ? 20 1 1 A DC 3 1_555 B DG 10 1_555 0.342 -0.031 -0.016 -14.788 9.927 -4.544 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.324 -0.015 0.127 16.739 8.890 -4.336 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B DG 8 1_555 0.285 -0.061 0.227 -16.767 24.556 -3.863 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DA 6 1_555 B DT 7 1_555 0.013 0.597 0.409 4.308 36.893 -23.263 6 A_DA6:DT7_B A 6 ? B 7 ? ? ? 1 A DT 9 1_555 B DA 6 1_555 0.253 0.321 -0.441 -13.078 -3.940 8.034 7 A_DT9:DA6_B A 9 ? B 6 ? ? ? 1 A DC 10 1_555 B DG 5 1_555 0.061 -0.481 1.820 -31.018 9.511 -7.150 8 A_DC10:DG5_B A 10 ? B 5 ? 19 1 1 A DG 11 1_555 B DC 4 1_555 -0.319 -0.146 0.769 8.820 12.094 -1.719 9 A_DG11:DC4_B A 11 ? B 4 ? 19 1 1 A DG 12 1_555 B DC 3 1_555 -0.309 -0.060 -0.120 8.609 12.246 -5.043 10 A_DG12:DC3_B A 12 ? B 3 ? 19 1 1 A DA 13 1_555 B DT 2 1_555 -0.006 -0.194 1.362 24.966 6.230 -6.049 11 A_DA13:DT2_B A 13 ? B 2 ? 20 1 1 A DC 14 1_555 B DG 1 1_555 0.452 -0.474 -1.074 3.070 18.967 -14.169 12 A_DC14:DG1_B A 14 ? B 1 ? 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 DC 1 1_555 B DG 12 1_555 A DA 2 1_555 B DT 11 1_555 -0.343 0.111 3.327 -4.280 -12.772 35.230 1.867 -0.037 3.122 -20.213 6.773 37.641 1 AA_DC1DA2:DT11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DA 2 1_555 B DT 11 1_555 A DC 3 1_555 B DG 10 1_555 -0.884 -0.322 5.976 6.096 -4.130 36.898 0.475 2.810 5.764 -6.446 -9.515 37.601 2 AA_DA2DC3:DG10DT11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.060 0.092 2.721 -0.716 -12.252 33.783 1.606 0.012 2.537 -20.271 1.185 35.882 3 AA_DC3DG4:DC9DG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 9 1_555 A DC 5 1_555 B DG 8 1_555 0.523 -1.276 4.880 -2.875 12.655 36.303 -4.180 -1.304 4.170 19.559 4.443 38.479 4 AA_DG4DC5:DG8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B DG 8 1_555 A DA 6 1_555 B DT 7 1_555 -1.867 0.199 4.119 1.378 -0.909 28.599 0.658 4.161 4.019 -1.839 -2.787 28.646 5 AA_DC5DA6:DT7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A DT 9 1_555 B DA 6 1_555 A DC 10 1_555 B DG 5 1_555 -1.464 0.353 4.846 -15.334 2.615 41.149 0.082 -0.326 5.068 3.570 20.937 43.872 6 AA_DT9DC10:DG5DA6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A DC 10 1_555 B DG 5 1_555 A DG 11 1_555 B DC 4 1_555 0.258 -0.007 2.409 2.885 -4.667 31.774 0.603 -0.085 2.399 -8.445 -5.220 32.232 7 AA_DC10DG11:DC4DG5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A DG 11 1_555 B DC 4 1_555 A DG 12 1_555 B DC 3 1_555 -0.056 0.218 3.913 5.490 8.031 35.611 -0.965 0.985 3.821 12.838 -8.777 36.874 8 AA_DG11DG12:DC3DC4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A DG 12 1_555 B DC 3 1_555 A DA 13 1_555 B DT 2 1_555 0.241 -0.154 3.261 -5.390 -2.592 36.741 0.101 -1.090 3.198 -4.079 8.481 37.208 9 AA_DG12DA13:DT2DC3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 A DA 13 1_555 B DT 2 1_555 A DC 14 1_555 B DG 1 1_555 -0.397 -0.005 5.545 7.789 -19.617 38.470 3.192 1.804 4.843 -27.407 -10.882 43.687 10 AA_DA13DC14:DG1DT2_BB A 13 ? B 2 ? A 14 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name ;SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI) ; _pdbx_entity_nonpoly.comp_id DDI #