data_1R4E # _entry.id 1R4E # _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 1R4E pdb_00001r4e 10.2210/pdb1r4e/pdb RCSB RCSB020422 ? ? WWPDB D_1000020422 ? ? # 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 2004-04-27 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-05-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' '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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_nmr_spectrometer 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' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1R4E _pdbx_database_status.recvd_initial_deposition_date 2003-10-06 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1P96 _pdbx_database_related.details 'The complexed structure of the bulge DNA and right-handed spicyclic compound' _pdbx_database_related.content_type unspecified # 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 ;Stereochemical control of small molecule binding to bulged DNA: comparison of structures of spirocyclic enantiomer-bulged DNA complexes. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 43 _citation.page_first 641 _citation.page_last 650 _citation.year 2004 _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 14730968 _citation.pdbx_database_id_DOI 10.1021/bi035824i # 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 ? # _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 # 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_ _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_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 DC A . n A 1 2 DA 2 2 2 DA DA A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DG 11 11 11 DG DG A . n A 1 12 DG 12 12 12 DG DG A . n A 1 13 DA 13 13 13 DA DA A . n A 1 14 DC 14 14 14 DC DC A . n B 2 1 DG 1 1 1 DG DG B . n B 2 2 DT 2 2 2 DT DT B . n B 2 3 DC 3 3 3 DC DC B . n B 2 4 DC 4 4 4 DC DC B . n B 2 5 DG 5 5 5 DG DG B . n B 2 6 DA 6 6 6 DA DA B . n B 2 7 DT 7 7 7 DT DT B . n B 2 8 DG 8 8 8 DG DG B . n B 2 9 DC 9 9 9 DC DC B . n B 2 10 DG 10 10 10 DG DG B . n B 2 11 DT 11 11 11 DT DT B . n B 2 12 DG 12 12 12 DG DG 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 15 _pdbx_nonpoly_scheme.auth_seq_num 15 _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 . # _cell.entry_id 1R4E _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 1R4E _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 1R4E _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 # _database_PDB_matrix.entry_id 1R4E _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1R4E _struct.title 'Solution structure of the Complex Formed between a Left-Handed Wedge-Shaped Spirocyclic Molecule and Bulged DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1R4E _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Wedge-shaped spirocyclic enantiomer-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 ? # 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 1R4E 1R4E ? ? ? 2 2 PDB 1R4E 1R4E ? ? ? # 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 1R4E A 1 ? 14 ? 1R4E 1 ? 14 ? 1 14 2 2 1R4E B 1 ? 12 ? 1R4E 1 ? 12 ? 1 12 # _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 # _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 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 9 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 9 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DA 13 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 13 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DA 13 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 13 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 14 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 14 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DC 14 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 14 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 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 15 ? 4 'BINDING SITE FOR RESIDUE DDI A 15' 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 DT A 9 ? DT A 9 . ? 1_555 ? 3 AC1 4 DA B 6 ? DA B 6 . ? 1_555 ? 4 AC1 4 DT B 7 ? DT B 7 . ? 1_555 ? # 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 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 2 2 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 3 3 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 4 4 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 5 5 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 6 6 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 7 7 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 8 8 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 9 9 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 10 10 "H2''" A DT 8 ? ? OP2 A DT 9 ? ? 1.51 # _struct_site_keywords.site_id 1 _struct_site_keywords.text INTERCALATION # _pdbx_nmr_ensemble.entry_id 1R4E _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 1R4E _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'all calculated structures submited have the least restraint violation and the lowst energy.' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '1.2 mM ent-DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer, 90% H2O/10% D2O, 99.96% D2O' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O; 99.96% D2O' # _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 and 0.1mM EDTA buffer' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # 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 CPSY' # _pdbx_nmr_details.entry_id 1R4E _pdbx_nmr_details.text 'This structure was determined using 2D homonuclear and heteronuclear techniques.' # _pdbx_nmr_refine.entry_id 1R4E _pdbx_nmr_refine.method 'distance geometry, simulated annealing' _pdbx_nmr_refine.details 'The structures are based on a total of 427 NOE restraints and 166 dihedral angle restraints.' _pdbx_nmr_refine.software_ordinal 1 # 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 # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DDI N N N N 71 DDI C27 C N R 72 DDI C28 C N R 73 DDI O4 O N N 74 DDI C29 C N S 75 DDI O5 O N N 76 DDI C30 C N R 77 DDI C31 C N N 78 DDI O6 O N N 79 DDI O7 O N N 80 DDI C26 C N R 81 DDI O3 O N N 82 DDI C25 C N S 83 DDI C24 C N N 84 DDI C12 C N S 85 DDI C11 C N S 86 DDI C23 C Y N 87 DDI C22 C Y N 88 DDI C21 C Y N 89 DDI C20 C Y N 90 DDI C19 C Y N 91 DDI C18 C Y N 92 DDI C17 C Y N 93 DDI C16 C Y N 94 DDI C15 C Y N 95 DDI C14 C Y N 96 DDI C13 C N N 97 DDI O2 O N N 98 DDI C9 C N S 99 DDI C10 C Y N 100 DDI C1 C Y N 101 DDI C2 C Y N 102 DDI C3 C Y N 103 DDI C4 C Y N 104 DDI C5 C Y N 105 DDI C6 C N N 106 DDI C7 C N N 107 DDI C8 C N N 108 DDI O1 O N N 109 DDI HN1 H N N 110 DDI HN2 H N N 111 DDI H27 H N N 112 DDI H28 H N N 113 DDI HO4 H N N 114 DDI H29 H N N 115 DDI HO5 H N N 116 DDI H30 H N N 117 DDI H31A H N N 118 DDI H31B H N N 119 DDI HO6 H N N 120 DDI H26 H N N 121 DDI H25 H N N 122 DDI H24A H N N 123 DDI H24B H N N 124 DDI H12 H N N 125 DDI H11 H N N 126 DDI H22 H N N 127 DDI H20 H N N 128 DDI H19 H N N 129 DDI H18 H N N 130 DDI H17 H N N 131 DDI H15 H N N 132 DDI H1 H N N 133 DDI H2 H N N 134 DDI H3 H N N 135 DDI H4 H N N 136 DDI H6A H N N 137 DDI H6B H N N 138 DDI H7A H N N 139 DDI H7B H N N 140 DG OP3 O N N 141 DG P P N N 142 DG OP1 O N N 143 DG OP2 O N N 144 DG "O5'" O N N 145 DG "C5'" C N N 146 DG "C4'" C N R 147 DG "O4'" O N N 148 DG "C3'" C N S 149 DG "O3'" O N N 150 DG "C2'" C N N 151 DG "C1'" C N R 152 DG N9 N Y N 153 DG C8 C Y N 154 DG N7 N Y N 155 DG C5 C Y N 156 DG C6 C N N 157 DG O6 O N N 158 DG N1 N N N 159 DG C2 C N N 160 DG N2 N N N 161 DG N3 N N N 162 DG C4 C Y N 163 DG HOP3 H N N 164 DG HOP2 H N N 165 DG "H5'" H N N 166 DG "H5''" H N N 167 DG "H4'" H N N 168 DG "H3'" H N N 169 DG "HO3'" H N N 170 DG "H2'" H N N 171 DG "H2''" H N N 172 DG "H1'" H N N 173 DG H8 H N N 174 DG H1 H N N 175 DG H21 H N N 176 DG H22 H N N 177 DT OP3 O N N 178 DT P P N N 179 DT OP1 O N N 180 DT OP2 O N N 181 DT "O5'" O N N 182 DT "C5'" C N N 183 DT "C4'" C N R 184 DT "O4'" O N N 185 DT "C3'" C N S 186 DT "O3'" O N N 187 DT "C2'" C N N 188 DT "C1'" C N R 189 DT N1 N N N 190 DT C2 C N N 191 DT O2 O N N 192 DT N3 N N N 193 DT C4 C N N 194 DT O4 O N N 195 DT C5 C N N 196 DT C7 C N N 197 DT C6 C N N 198 DT HOP3 H N N 199 DT HOP2 H N N 200 DT "H5'" H N N 201 DT "H5''" H N N 202 DT "H4'" H N N 203 DT "H3'" H N N 204 DT "HO3'" H N N 205 DT "H2'" H N N 206 DT "H2''" H N N 207 DT "H1'" H N N 208 DT H3 H N N 209 DT H71 H N N 210 DT H72 H N N 211 DT H73 H N N 212 DT H6 H N N 213 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DDI N C27 sing N N 74 DDI N HN1 sing N N 75 DDI N HN2 sing N N 76 DDI C27 C28 sing N N 77 DDI C27 C26 sing N N 78 DDI C27 H27 sing N N 79 DDI C28 O4 sing N N 80 DDI C28 C29 sing N N 81 DDI C28 H28 sing N N 82 DDI O4 HO4 sing N N 83 DDI C29 O5 sing N N 84 DDI C29 C30 sing N N 85 DDI C29 H29 sing N N 86 DDI O5 HO5 sing N N 87 DDI C30 C31 sing N N 88 DDI C30 O7 sing N N 89 DDI C30 H30 sing N N 90 DDI C31 O6 sing N N 91 DDI C31 H31A sing N N 92 DDI C31 H31B sing N N 93 DDI O6 HO6 sing N N 94 DDI O7 C26 sing N N 95 DDI C26 O3 sing N N 96 DDI C26 H26 sing N N 97 DDI O3 C25 sing N N 98 DDI C25 C24 sing N N 99 DDI C25 C9 sing N N 100 DDI C25 H25 sing N N 101 DDI C24 C12 sing N N 102 DDI C24 H24A sing N N 103 DDI C24 H24B sing N N 104 DDI C12 C11 sing N N 105 DDI C12 C13 sing N N 106 DDI C12 H12 sing N N 107 DDI C11 C23 sing N N 108 DDI C11 C9 sing N N 109 DDI C11 H11 sing N N 110 DDI C23 C22 doub Y N 111 DDI C23 C14 sing Y N 112 DDI C22 C21 sing Y N 113 DDI C22 H22 sing N N 114 DDI C21 C20 doub Y N 115 DDI C21 C16 sing Y N 116 DDI C20 C19 sing Y N 117 DDI C20 H20 sing N N 118 DDI C19 C18 doub Y N 119 DDI C19 H19 sing N N 120 DDI C18 C17 sing Y N 121 DDI C18 H18 sing N N 122 DDI C17 C16 doub Y N 123 DDI C17 H17 sing N N 124 DDI C16 C15 sing Y N 125 DDI C15 C14 doub Y N 126 DDI C15 H15 sing N N 127 DDI C14 C13 sing N N 128 DDI C13 O2 doub N N 129 DDI C9 C10 sing N N 130 DDI C9 C8 sing N N 131 DDI C10 C1 doub Y N 132 DDI C10 C5 sing Y N 133 DDI C1 C2 sing Y N 134 DDI C1 H1 sing N N 135 DDI C2 C3 doub Y N 136 DDI C2 H2 sing N N 137 DDI C3 C4 sing Y N 138 DDI C3 H3 sing N N 139 DDI C4 C5 doub Y N 140 DDI C4 H4 sing N N 141 DDI C5 C6 sing N N 142 DDI C6 C7 sing N N 143 DDI C6 H6A sing N N 144 DDI C6 H6B sing N N 145 DDI C7 C8 sing N N 146 DDI C7 H7A sing N N 147 DDI C7 H7B sing N N 148 DDI C8 O1 doub N N 149 DG OP3 P sing N N 150 DG OP3 HOP3 sing N N 151 DG P OP1 doub N N 152 DG P OP2 sing N N 153 DG P "O5'" sing N N 154 DG OP2 HOP2 sing N N 155 DG "O5'" "C5'" sing N N 156 DG "C5'" "C4'" sing N N 157 DG "C5'" "H5'" sing N N 158 DG "C5'" "H5''" sing N N 159 DG "C4'" "O4'" sing N N 160 DG "C4'" "C3'" sing N N 161 DG "C4'" "H4'" sing N N 162 DG "O4'" "C1'" sing N N 163 DG "C3'" "O3'" sing N N 164 DG "C3'" "C2'" sing N N 165 DG "C3'" "H3'" sing N N 166 DG "O3'" "HO3'" sing N N 167 DG "C2'" "C1'" sing N N 168 DG "C2'" "H2'" sing N N 169 DG "C2'" "H2''" sing N N 170 DG "C1'" N9 sing N N 171 DG "C1'" "H1'" sing N N 172 DG N9 C8 sing Y N 173 DG N9 C4 sing Y N 174 DG C8 N7 doub Y N 175 DG C8 H8 sing N N 176 DG N7 C5 sing Y N 177 DG C5 C6 sing N N 178 DG C5 C4 doub Y N 179 DG C6 O6 doub N N 180 DG C6 N1 sing N N 181 DG N1 C2 sing N N 182 DG N1 H1 sing N N 183 DG C2 N2 sing N N 184 DG C2 N3 doub N N 185 DG N2 H21 sing N N 186 DG N2 H22 sing N N 187 DG N3 C4 sing N N 188 DT OP3 P sing N N 189 DT OP3 HOP3 sing N N 190 DT P OP1 doub N N 191 DT P OP2 sing N N 192 DT P "O5'" sing N N 193 DT OP2 HOP2 sing N N 194 DT "O5'" "C5'" sing N N 195 DT "C5'" "C4'" sing N N 196 DT "C5'" "H5'" sing N N 197 DT "C5'" "H5''" sing N N 198 DT "C4'" "O4'" sing N N 199 DT "C4'" "C3'" sing N N 200 DT "C4'" "H4'" sing N N 201 DT "O4'" "C1'" sing N N 202 DT "C3'" "O3'" sing N N 203 DT "C3'" "C2'" sing N N 204 DT "C3'" "H3'" sing N N 205 DT "O3'" "HO3'" sing N N 206 DT "C2'" "C1'" sing N N 207 DT "C2'" "H2'" sing N N 208 DT "C2'" "H2''" sing N N 209 DT "C1'" N1 sing N N 210 DT "C1'" "H1'" sing N N 211 DT N1 C2 sing N N 212 DT N1 C6 sing N N 213 DT C2 O2 doub N N 214 DT C2 N3 sing N N 215 DT N3 C4 sing N N 216 DT N3 H3 sing N N 217 DT C4 O4 doub N N 218 DT C4 C5 sing N N 219 DT C5 C7 sing N N 220 DT C5 C6 doub N N 221 DT C7 H71 sing N N 222 DT C7 H72 sing N N 223 DT C7 H73 sing N N 224 DT C6 H6 sing N N 225 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1R4E 'double helix' 1R4E '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 -0.286 -0.478 -1.135 18.794 27.311 -18.526 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DA 2 1_555 B DT 11 1_555 -0.245 -0.098 0.819 8.681 16.990 -0.556 2 A_DA2:DT11_B A 2 ? B 11 ? 20 1 1 A DC 3 1_555 B DG 10 1_555 0.266 -0.162 -0.413 -10.228 18.889 -7.374 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.329 -0.097 -0.051 12.314 21.088 -4.812 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B DG 8 1_555 0.298 -0.169 -0.321 0.521 19.467 -4.283 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DA 6 1_555 B DT 7 1_555 -0.253 0.130 0.463 26.629 14.916 -5.490 6 A_DA6:DT7_B A 6 ? B 7 ? 20 1 1 A DT 9 1_555 B DA 6 1_555 0.874 -0.095 -0.253 -9.165 5.493 -8.471 7 A_DT9:DA6_B A 9 ? B 6 ? 20 1 1 A DC 10 1_555 B DG 5 1_555 0.159 -0.276 1.195 -13.872 2.623 -6.711 8 A_DC10:DG5_B A 10 ? B 5 ? 19 1 1 A DG 11 1_555 B DC 4 1_555 -0.324 -0.069 0.190 9.278 16.499 -3.166 9 A_DG11:DC4_B A 11 ? B 4 ? 19 1 1 A DG 12 1_555 B DC 3 1_555 -0.346 -0.096 0.111 8.491 19.903 -3.033 10 A_DG12:DC3_B A 12 ? B 3 ? 19 1 1 A DA 13 1_555 B DT 2 1_555 0.053 -0.118 0.071 6.651 23.127 -1.601 11 A_DA13:DT2_B A 13 ? B 2 ? 20 1 1 A DC 14 1_555 B DG 1 1_555 0.162 -0.321 -0.161 -23.322 47.957 -9.272 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 1.135 -1.080 5.490 -11.162 -18.103 32.413 2.219 -4.093 4.808 -28.881 17.807 38.610 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 -0.798 -0.620 5.180 3.899 -3.414 34.517 -0.216 2.264 5.099 -5.714 -6.524 34.892 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 0.348 -0.769 2.931 -2.004 -3.560 30.646 -0.817 -1.005 2.971 -6.698 3.771 30.911 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 0.073 -1.122 4.461 1.898 2.447 33.186 -2.506 0.299 4.367 4.272 -3.315 33.326 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 -0.032 -0.275 3.573 -0.795 -11.823 31.929 1.627 -0.086 3.454 -20.626 1.386 34.003 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 0.530 0.202 4.243 -4.604 8.075 36.822 -1.027 -1.577 4.102 12.540 7.149 37.937 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 0.374 -0.734 3.193 2.581 -8.537 30.622 0.237 -0.205 3.293 -15.750 -4.763 31.865 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 0.402 -1.054 3.738 1.238 5.244 30.631 -3.091 -0.485 3.527 9.832 -2.321 31.091 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 0.246 -0.853 4.276 -0.182 -0.263 32.665 -1.457 -0.480 4.281 -0.468 0.324 32.667 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 -0.799 -1.581 6.221 -2.379 -5.271 26.648 -0.772 0.531 6.453 -11.268 5.086 27.257 10 AA_DA13DC14:DG1DT2_BB A 13 ? B 2 ? A 14 ? B 1 ? # 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 # _atom_sites.entry_id 1R4E _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_