data_1MK6 # _entry.id 1MK6 # _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 1MK6 pdb_00001mk6 10.2210/pdb1mk6/pdb RCSB RCSB016974 ? ? WWPDB D_1000016974 ? ? # 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 2002-10-16 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2019-01-30 5 'Structure model' 2 1 2024-05-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Non-polymer description' 8 4 'Structure model' 'Polymer sequence' 9 4 'Structure model' 'Source and taxonomy' 10 4 'Structure model' 'Structure summary' 11 5 'Structure model' 'Data collection' 12 5 'Structure model' 'Database references' 13 5 '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' atom_site 2 4 'Structure model' chem_comp 3 4 'Structure model' entity 4 4 'Structure model' entity_poly 5 4 'Structure model' entity_poly_seq 6 4 'Structure model' ndb_struct_conf_na 7 4 'Structure model' ndb_struct_na_base_pair_step 8 4 'Structure model' pdbx_entity_nonpoly 9 4 'Structure model' pdbx_entity_src_syn 10 4 'Structure model' pdbx_nonpoly_scheme 11 4 'Structure model' pdbx_poly_seq_scheme 12 4 'Structure model' pdbx_struct_assembly 13 4 'Structure model' pdbx_struct_mod_residue 14 4 'Structure model' pdbx_struct_oper_list 15 4 'Structure model' pdbx_validate_rmsd_angle 16 4 'Structure model' struct_asym 17 4 'Structure model' struct_conn 18 4 'Structure model' struct_ref 19 5 'Structure model' chem_comp_atom 20 5 'Structure model' chem_comp_bond 21 5 'Structure model' database_2 22 5 'Structure model' pdbx_nmr_software 23 5 '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' '_atom_site.Cartn_x' 2 4 'Structure model' '_atom_site.Cartn_y' 3 4 'Structure model' '_atom_site.Cartn_z' 4 4 'Structure model' '_atom_site.auth_asym_id' 5 4 'Structure model' '_atom_site.auth_atom_id' 6 4 'Structure model' '_atom_site.auth_comp_id' 7 4 'Structure model' '_atom_site.auth_seq_id' 8 4 'Structure model' '_atom_site.group_PDB' 9 4 'Structure model' '_atom_site.label_asym_id' 10 4 'Structure model' '_atom_site.label_atom_id' 11 4 'Structure model' '_atom_site.label_comp_id' 12 4 'Structure model' '_atom_site.label_entity_id' 13 4 'Structure model' '_atom_site.label_seq_id' 14 4 'Structure model' '_atom_site.type_symbol' 15 4 'Structure model' '_chem_comp.formula' 16 4 'Structure model' '_chem_comp.formula_weight' 17 4 'Structure model' '_chem_comp.id' 18 4 'Structure model' '_chem_comp.mon_nstd_flag' 19 4 'Structure model' '_chem_comp.name' 20 4 'Structure model' '_chem_comp.type' 21 4 'Structure model' '_entity_poly.nstd_monomer' 22 4 'Structure model' '_entity_poly.pdbx_seq_one_letter_code' 23 4 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 24 4 'Structure model' '_entity_poly_seq.mon_id' 25 4 'Structure model' '_ndb_struct_na_base_pair_step.roll' 26 4 'Structure model' '_pdbx_poly_seq_scheme.mon_id' 27 4 'Structure model' '_pdbx_poly_seq_scheme.pdb_mon_id' 28 4 'Structure model' '_struct_ref.pdbx_align_begin' 29 5 'Structure model' '_database_2.pdbx_DOI' 30 5 'Structure model' '_database_2.pdbx_database_accession' 31 5 'Structure model' '_pdbx_nmr_software.name' 32 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1MK6 _pdbx_database_status.recvd_initial_deposition_date 2002-08-28 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1MKL _pdbx_database_related.details ;NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE ; _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Giri, I.' 1 'Johnston, D.S.' 2 'Stone, M.P.' 3 # _citation.id primary _citation.title ;MISPAIRING OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT WITH DEOXYADENOSINE RESULTS IN EXTRUSION OF THE MISMATCHED DA TOWARD THE MAJOR GROOVE ; _citation.journal_abbrev Biochemistry _citation.journal_volume 41 _citation.page_first 5462 _citation.page_last 5472 _citation.year 2002 _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 11969407 _citation.pdbx_database_id_DOI 10.1021/bi012116t # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Giri, I.' 1 ? primary 'Johnston, D.S.' 2 ? primary 'Stone, M.P.' 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(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'" 3003.993 1 ? ? ? ? 2 polymer syn "5'-D(*AP*GP*AP*TP*AP*GP*AP*TP*GP*T)-3'" 3108.065 1 ? ? ? ? 3 non-polymer syn '8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1' 330.289 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 '(DA)(DC)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DT)' ACATCGATCT A ? 2 polydeoxyribonucleotide no no '(DA)(DG)(DA)(DT)(DA)(DG)(DA)(DT)(DG)(DT)' AGATAGATGT B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name '8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1' _pdbx_entity_nonpoly.comp_id AFN # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DC n 1 3 DA n 1 4 DT n 1 5 DC n 1 6 DG n 1 7 DA n 1 8 DT n 1 9 DC n 1 10 DT n 2 1 DA n 2 2 DG n 2 3 DA n 2 4 DT n 2 5 DA n 2 6 DG n 2 7 DA n 2 8 DT n 2 9 DG n 2 10 DT 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 1 10 'synthetic construct' ? 32630 ? 2 1 sample 1 10 'synthetic construct' ? 32630 ? # 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 AFN non-polymer . '8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1' ? 'C17 H14 O7' 330.289 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 # 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 DA 1 1 1 DA A A . n A 1 2 DC 2 2 2 DC C 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 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG X A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DT 10 10 10 DT T A . n B 2 1 DA 1 11 11 DA A B . n B 2 2 DG 2 12 12 DG G B . n B 2 3 DA 3 13 13 DA A B . n B 2 4 DT 4 14 14 DT T B . n B 2 5 DA 5 15 15 DA A B . n B 2 6 DG 6 16 16 DG G 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 DG 9 19 19 DG G B . n B 2 10 DT 10 20 20 DT T B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id AFN _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 11 _pdbx_nonpoly_scheme.auth_seq_num 6 _pdbx_nonpoly_scheme.pdb_mon_id AFN _pdbx_nonpoly_scheme.auth_mon_id X _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _exptl.entry_id 1MK6 _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.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? # _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 1MK6 _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 1MK6 _struct.title 'SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1MK6 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'AFLATOXIN B1- Guanine Adduct Opposite an Adenine, mimicking GA Transition, 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.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 1MK6 1MK6 ? 1 ? 1 2 PDB 1MK6 1MK6 ? 2 ? 1 # 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 1MK6 A 1 ? 10 ? 1MK6 1 ? 10 ? 1 10 2 2 1MK6 B 1 ? 10 ? 1MK6 11 ? 20 ? 11 20 # _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 ? _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_ _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 none ? A DG 6 N7 ? ? ? 1_555 C AFN . C8A ? ? A DG 6 A AFN 11 1_555 ? ? ? ? ? ? ? 1.507 sing ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 10 N3 ? ? A DA 1 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 10 O4 ? ? A DA 1 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 8 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 8 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 9 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 9 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 9 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 10 B DA 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 10 B DA 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 N1 A DA 1 ? ? C6 A DA 1 ? ? N6 A DA 1 ? ? 114.36 118.60 -4.24 0.60 N 2 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.15 108.30 1.85 0.30 N 3 1 C5 A DA 3 ? ? C6 A DA 3 ? ? N1 A DA 3 ? ? 120.71 117.70 3.01 0.50 N 4 1 N1 A DA 3 ? ? C6 A DA 3 ? ? N6 A DA 3 ? ? 114.16 118.60 -4.44 0.60 N 5 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 118.34 122.90 -4.56 0.60 N 6 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 111.62 108.30 3.32 0.30 N 7 1 N1 A DA 7 ? ? C6 A DA 7 ? ? N6 A DA 7 ? ? 114.40 118.60 -4.20 0.60 N 8 1 C6 A DT 8 ? ? C5 A DT 8 ? ? C7 A DT 8 ? ? 118.02 122.90 -4.88 0.60 N 9 1 N1 A DC 9 ? ? C2 A DC 9 ? ? O2 A DC 9 ? ? 122.78 118.90 3.88 0.60 N 10 1 N3 A DC 9 ? ? C2 A DC 9 ? ? O2 A DC 9 ? ? 117.41 121.90 -4.49 0.70 N 11 1 "O4'" A DT 10 ? ? "C1'" A DT 10 ? ? N1 A DT 10 ? ? 111.99 108.30 3.69 0.30 N 12 1 C6 A DT 10 ? ? C5 A DT 10 ? ? C7 A DT 10 ? ? 118.91 122.90 -3.99 0.60 N 13 1 N1 B DA 11 ? ? C6 B DA 11 ? ? N6 B DA 11 ? ? 114.23 118.60 -4.37 0.60 N 14 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.78 108.30 2.48 0.30 N 15 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 112.16 108.30 3.86 0.30 N 16 1 C6 B DT 14 ? ? C5 B DT 14 ? ? C7 B DT 14 ? ? 118.29 122.90 -4.61 0.60 N 17 1 "O4'" B DA 15 ? ? "C1'" B DA 15 ? ? N9 B DA 15 ? ? 111.69 108.30 3.39 0.30 N 18 1 C5 B DA 15 ? ? C6 B DA 15 ? ? N1 B DA 15 ? ? 120.85 117.70 3.15 0.50 N 19 1 N1 B DA 15 ? ? C6 B DA 15 ? ? N6 B DA 15 ? ? 114.43 118.60 -4.17 0.60 N 20 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 110.90 108.30 2.60 0.30 N 21 1 C6 B DT 20 ? ? C5 B DT 20 ? ? C7 B DT 20 ? ? 119.16 122.90 -3.74 0.60 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DA _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 15 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.102 _pdbx_validate_planes.type 'SIDE CHAIN' # _pdbx_nmr_ensemble.entry_id 1MK6 _pdbx_nmr_ensemble.conformers_calculated_total_number 20 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ;Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and counterions. Solvent, and Counterion co-ordinates are NOT being reported, only the Duplex DNA. Before Solvating and Addition of Counter IONS, 20 final structures were calculated using XPLOR. The final averaged energy minimized structure was solvated, and the counter Ions were added to it. Then MD was ran for 1.4 ns time scale to obtain final structure. ; _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 1MK6 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria ? # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '80 OD of d(ACATCAFBGATCT)d(AGATAGATGT) solution in NMR Buffer' _pdbx_nmr_sample_details.solvent_system ;For observation of nonexchangeable protons, the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O. For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O. Most experiments were performed at 5 C. Spectra of exchangeable protons were obtained at 0 C. ; # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 278 ATM 7.4 '0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O' ? K 2 273 ATM 7.4 ;For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O, buffer, containing 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.4 ; ? 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 P-COSY 5 1 1 T1 # _pdbx_nmr_details.entry_id 1MK6 _pdbx_nmr_details.text ;40 Structures were calculated starting from B and A form DNA. 20 closely convergent from both was averaged, and RMSD value was checked. The final averaged structure was calculated by averaging Final A and Final B, and after energy Minimization. This energy minimized structure was solvated, and explicit counterions were added. In all, 17 Na+ ions were added to neutralize the system using the Leap module in AMBER 6.0. The SHAKE algorithm constrained bonds involving protons to a tolerance of 0.0005 . A 1 fs time step was used. The rMD calculations were run for 1.4 ns, and coordinates were captured every 200 ps. The emergent structure from AMBER is Being reported ; # _pdbx_nmr_refine.entry_id 1MK6 _pdbx_nmr_refine.method ;distance geometry : MardiGras; simulated annealing molecular dynamics : XPLOR; Average structure Calculation Addition of Solvent, and Counterions : AMBER; simulated annealing and Molecular Dynamics matrix relaxation : CORMA; ; _pdbx_nmr_refine.details ;There were 329 experimental distance restraints derived from nonexchangeable 1H NOEs by MARDIGRAS. These consisted of 181 intranucleotide restraints, 110 internucleotide restraints, and 38 adduct-DNA 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 Felix '97, 2000' processing 'Accelyris, Inc., San Diego, CA' 1 XwinNMR 4.0 collection Bruker 2 MARDIGRAS 3.2 'data analysis' 'Borgias, B. A., and James, T. L. (1990) J. Magn. Reson. 87, 475-487' 3 X-PLOR 3.1 refinement A.T.Brunger 4 Amber 6.0 'structure solution' 'Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) J. Phys. Chem. 40, 10269-10280' 5 CORMA 4.0 'data analysis' 'Keepers, J. W., and James, T. L. (1984) J. Magn. Reson. 57, 404-426.' 6 'Insight II' 2000 'structure solution' 'Accelyris, Inc., San Diego, CA' 7 'GAUSSIAN 98' 1998 processing 'Frisch, M. J., Trucks, G. W., et al. (1998) Gaussian 98, Gaussian Inc., Pittsburgh, PA.' 8 # 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 AFN C8A C N N 1 AFN C9 C N R 2 AFN O9 O N N 3 AFN C9A C N R 4 AFN C9B C Y N 5 AFN O7 O N N 6 AFN C6A C N R 7 AFN O6A O N N 8 AFN C5A C Y N 9 AFN C5B C Y N 10 AFN C4B C Y N 11 AFN O4 O N N 12 AFN CM C N N 13 AFN C4A C Y N 14 AFN C10 C Y N 15 AFN O10 O Y N 16 AFN C11 C Y N 17 AFN O11 O N N 18 AFN C12 C Y N 19 AFN C3A C Y N 20 AFN C3 C N N 21 AFN C2A C N N 22 AFN C1 C N N 23 AFN O1 O N N 24 AFN H8A2 H N N 25 AFN H8A H N N 26 AFN H9 H N N 27 AFN HO9 H N N 28 AFN H9A H N N 29 AFN H6A H N N 30 AFN H5B H N N 31 AFN HM1 H N N 32 AFN HM2 H N N 33 AFN HM3 H N N 34 AFN H31 H N N 35 AFN H32 H N N 36 AFN H2A1 H N N 37 AFN H2A2 H N N 38 DA OP3 O N N 39 DA P P N N 40 DA OP1 O N N 41 DA OP2 O N N 42 DA "O5'" O N N 43 DA "C5'" C N N 44 DA "C4'" C N R 45 DA "O4'" O N N 46 DA "C3'" C N S 47 DA "O3'" O N N 48 DA "C2'" C N N 49 DA "C1'" C N R 50 DA N9 N Y N 51 DA C8 C Y N 52 DA N7 N Y N 53 DA C5 C Y N 54 DA C6 C Y N 55 DA N6 N N N 56 DA N1 N Y N 57 DA C2 C Y N 58 DA N3 N Y N 59 DA C4 C Y N 60 DA HOP3 H N N 61 DA HOP2 H N N 62 DA "H5'" H N N 63 DA "H5''" H N N 64 DA "H4'" H N N 65 DA "H3'" H N N 66 DA "HO3'" H N N 67 DA "H2'" H N N 68 DA "H2''" H N N 69 DA "H1'" H N N 70 DA H8 H N N 71 DA H61 H N N 72 DA H62 H N N 73 DA H2 H N N 74 DC OP3 O N N 75 DC P P N N 76 DC OP1 O N N 77 DC OP2 O N N 78 DC "O5'" O N N 79 DC "C5'" C N N 80 DC "C4'" C N R 81 DC "O4'" O N N 82 DC "C3'" C N S 83 DC "O3'" O N N 84 DC "C2'" C N N 85 DC "C1'" C N R 86 DC N1 N N N 87 DC C2 C N N 88 DC O2 O N N 89 DC N3 N N N 90 DC C4 C N N 91 DC N4 N N N 92 DC C5 C N N 93 DC C6 C N N 94 DC HOP3 H N N 95 DC HOP2 H N N 96 DC "H5'" H N N 97 DC "H5''" H N N 98 DC "H4'" H N N 99 DC "H3'" H N N 100 DC "HO3'" H N N 101 DC "H2'" H N N 102 DC "H2''" H N N 103 DC "H1'" H N N 104 DC H41 H N N 105 DC H42 H N N 106 DC H5 H N N 107 DC H6 H N N 108 DG OP3 O N N 109 DG P P N N 110 DG OP1 O N N 111 DG OP2 O N N 112 DG "O5'" O N N 113 DG "C5'" C N N 114 DG "C4'" C N R 115 DG "O4'" O N N 116 DG "C3'" C N S 117 DG "O3'" O N N 118 DG "C2'" C N N 119 DG "C1'" C N R 120 DG N9 N Y N 121 DG C8 C Y N 122 DG N7 N Y N 123 DG C5 C Y N 124 DG C6 C N N 125 DG O6 O N N 126 DG N1 N N N 127 DG C2 C N N 128 DG N2 N N N 129 DG N3 N N N 130 DG C4 C Y N 131 DG HOP3 H N N 132 DG HOP2 H N N 133 DG "H5'" H N N 134 DG "H5''" H N N 135 DG "H4'" H N N 136 DG "H3'" H N N 137 DG "HO3'" H N N 138 DG "H2'" H N N 139 DG "H2''" H N N 140 DG "H1'" H N N 141 DG H8 H N N 142 DG H1 H N N 143 DG H21 H N N 144 DG H22 H N N 145 DT OP3 O N N 146 DT P P N N 147 DT OP1 O N N 148 DT OP2 O N N 149 DT "O5'" O N N 150 DT "C5'" C N N 151 DT "C4'" C N R 152 DT "O4'" O N N 153 DT "C3'" C N S 154 DT "O3'" O N N 155 DT "C2'" C N N 156 DT "C1'" C N R 157 DT N1 N N N 158 DT C2 C N N 159 DT O2 O N N 160 DT N3 N N N 161 DT C4 C N N 162 DT O4 O N N 163 DT C5 C N N 164 DT C7 C N N 165 DT C6 C N N 166 DT HOP3 H N N 167 DT HOP2 H N N 168 DT "H5'" H N N 169 DT "H5''" H N N 170 DT "H4'" H N N 171 DT "H3'" H N N 172 DT "HO3'" H N N 173 DT "H2'" H N N 174 DT "H2''" H N N 175 DT "H1'" H N N 176 DT H3 H N N 177 DT H71 H N N 178 DT H72 H N N 179 DT H73 H N N 180 DT H6 H N N 181 # 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 AFN C8A C9 sing N N 1 AFN C8A O7 sing N N 2 AFN C8A H8A2 sing N N 3 AFN C8A H8A sing N N 4 AFN C9 O9 sing N N 5 AFN C9 C9A sing N N 6 AFN C9 H9 sing N N 7 AFN O9 HO9 sing N N 8 AFN C9A C9B sing N N 9 AFN C9A C6A sing N N 10 AFN C9A H9A sing N N 11 AFN C9B C5A doub Y N 12 AFN C9B C10 sing Y N 13 AFN O7 C6A sing N N 14 AFN C6A O6A sing N N 15 AFN C6A H6A sing N N 16 AFN O6A C5A sing N N 17 AFN C5A C5B sing Y N 18 AFN C5B C4B doub Y N 19 AFN C5B H5B sing N N 20 AFN C4B O4 sing N N 21 AFN C4B C4A sing Y N 22 AFN O4 CM sing N N 23 AFN CM HM1 sing N N 24 AFN CM HM2 sing N N 25 AFN CM HM3 sing N N 26 AFN C4A C10 doub Y N 27 AFN C4A C3A sing Y N 28 AFN C10 O10 sing Y N 29 AFN O10 C11 sing Y N 30 AFN C11 O11 doub N N 31 AFN C11 C12 sing Y N 32 AFN C12 C3A doub Y N 33 AFN C12 C1 sing N N 34 AFN C3A C3 sing N N 35 AFN C3 C2A sing N N 36 AFN C3 H31 sing N N 37 AFN C3 H32 sing N N 38 AFN C2A C1 sing N N 39 AFN C2A H2A1 sing N N 40 AFN C2A H2A2 sing N N 41 AFN C1 O1 doub N N 42 DA OP3 P sing N N 43 DA OP3 HOP3 sing N N 44 DA P OP1 doub N N 45 DA P OP2 sing N N 46 DA P "O5'" sing N N 47 DA OP2 HOP2 sing N N 48 DA "O5'" "C5'" sing N N 49 DA "C5'" "C4'" sing N N 50 DA "C5'" "H5'" sing N N 51 DA "C5'" "H5''" sing N N 52 DA "C4'" "O4'" sing N N 53 DA "C4'" "C3'" sing N N 54 DA "C4'" "H4'" sing N N 55 DA "O4'" "C1'" sing N N 56 DA "C3'" "O3'" sing N N 57 DA "C3'" "C2'" sing N N 58 DA "C3'" "H3'" sing N N 59 DA "O3'" "HO3'" sing N N 60 DA "C2'" "C1'" sing N N 61 DA "C2'" "H2'" sing N N 62 DA "C2'" "H2''" sing N N 63 DA "C1'" N9 sing N N 64 DA "C1'" "H1'" sing N N 65 DA N9 C8 sing Y N 66 DA N9 C4 sing Y N 67 DA C8 N7 doub Y N 68 DA C8 H8 sing N N 69 DA N7 C5 sing Y N 70 DA C5 C6 sing Y N 71 DA C5 C4 doub Y N 72 DA C6 N6 sing N N 73 DA C6 N1 doub Y N 74 DA N6 H61 sing N N 75 DA N6 H62 sing N N 76 DA N1 C2 sing Y N 77 DA C2 N3 doub Y N 78 DA C2 H2 sing N N 79 DA N3 C4 sing Y N 80 DC OP3 P sing N N 81 DC OP3 HOP3 sing N N 82 DC P OP1 doub N N 83 DC P OP2 sing N N 84 DC P "O5'" sing N N 85 DC OP2 HOP2 sing N N 86 DC "O5'" "C5'" sing N N 87 DC "C5'" "C4'" sing N N 88 DC "C5'" "H5'" sing N N 89 DC "C5'" "H5''" sing N N 90 DC "C4'" "O4'" sing N N 91 DC "C4'" "C3'" sing N N 92 DC "C4'" "H4'" sing N N 93 DC "O4'" "C1'" sing N N 94 DC "C3'" "O3'" sing N N 95 DC "C3'" "C2'" sing N N 96 DC "C3'" "H3'" sing N N 97 DC "O3'" "HO3'" sing N N 98 DC "C2'" "C1'" sing N N 99 DC "C2'" "H2'" sing N N 100 DC "C2'" "H2''" sing N N 101 DC "C1'" N1 sing N N 102 DC "C1'" "H1'" sing N N 103 DC N1 C2 sing N N 104 DC N1 C6 sing N N 105 DC C2 O2 doub N N 106 DC C2 N3 sing N N 107 DC N3 C4 doub N N 108 DC C4 N4 sing N N 109 DC C4 C5 sing N N 110 DC N4 H41 sing N N 111 DC N4 H42 sing N N 112 DC C5 C6 doub N N 113 DC C5 H5 sing N N 114 DC C6 H6 sing N N 115 DG OP3 P sing N N 116 DG OP3 HOP3 sing N N 117 DG P OP1 doub N N 118 DG P OP2 sing N N 119 DG P "O5'" sing N N 120 DG OP2 HOP2 sing N N 121 DG "O5'" "C5'" sing N N 122 DG "C5'" "C4'" sing N N 123 DG "C5'" "H5'" sing N N 124 DG "C5'" "H5''" sing N N 125 DG "C4'" "O4'" sing N N 126 DG "C4'" "C3'" sing N N 127 DG "C4'" "H4'" sing N N 128 DG "O4'" "C1'" sing N N 129 DG "C3'" "O3'" sing N N 130 DG "C3'" "C2'" sing N N 131 DG "C3'" "H3'" sing N N 132 DG "O3'" "HO3'" sing N N 133 DG "C2'" "C1'" sing N N 134 DG "C2'" "H2'" sing N N 135 DG "C2'" "H2''" sing N N 136 DG "C1'" N9 sing N N 137 DG "C1'" "H1'" sing N N 138 DG N9 C8 sing Y N 139 DG N9 C4 sing Y N 140 DG C8 N7 doub Y N 141 DG C8 H8 sing N N 142 DG N7 C5 sing Y N 143 DG C5 C6 sing N N 144 DG C5 C4 doub Y N 145 DG C6 O6 doub N N 146 DG C6 N1 sing N N 147 DG N1 C2 sing N N 148 DG N1 H1 sing N N 149 DG C2 N2 sing N N 150 DG C2 N3 doub N N 151 DG N2 H21 sing N N 152 DG N2 H22 sing N N 153 DG N3 C4 sing N N 154 DT OP3 P sing N N 155 DT OP3 HOP3 sing N N 156 DT P OP1 doub N N 157 DT P OP2 sing N N 158 DT P "O5'" sing N N 159 DT OP2 HOP2 sing N N 160 DT "O5'" "C5'" sing N N 161 DT "C5'" "C4'" sing N N 162 DT "C5'" "H5'" sing N N 163 DT "C5'" "H5''" sing N N 164 DT "C4'" "O4'" sing N N 165 DT "C4'" "C3'" sing N N 166 DT "C4'" "H4'" sing N N 167 DT "O4'" "C1'" sing N N 168 DT "C3'" "O3'" sing N N 169 DT "C3'" "C2'" sing N N 170 DT "C3'" "H3'" sing N N 171 DT "O3'" "HO3'" sing N N 172 DT "C2'" "C1'" sing N N 173 DT "C2'" "H2'" sing N N 174 DT "C2'" "H2''" sing N N 175 DT "C1'" N1 sing N N 176 DT "C1'" "H1'" sing N N 177 DT N1 C2 sing N N 178 DT N1 C6 sing N N 179 DT C2 O2 doub N N 180 DT C2 N3 sing N N 181 DT N3 C4 sing N N 182 DT N3 H3 sing N N 183 DT C4 O4 doub N N 184 DT C4 C5 sing N N 185 DT C5 C7 sing N N 186 DT C5 C6 doub N N 187 DT C7 H71 sing N N 188 DT C7 H72 sing N N 189 DT C7 H73 sing N N 190 DT C6 H6 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1MK6 'double helix' 1MK6 '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 DA 1 1_555 B DT 10 1_555 0.302 -0.135 0.966 23.636 -15.373 -3.284 1 A_DA1:DT20_B A 1 ? B 20 ? 20 1 1 A DC 2 1_555 B DG 9 1_555 0.239 -0.148 0.126 7.918 -12.410 -0.412 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DA 3 1_555 B DT 8 1_555 0.343 -0.063 -0.096 -10.484 -3.413 -0.790 3 A_DA3:DT18_B A 3 ? B 18 ? 20 1 1 A DT 4 1_555 B DA 7 1_555 0.110 -0.104 -0.069 -3.645 1.184 0.480 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DC 5 1_555 B DG 6 1_555 0.069 -0.160 -0.236 7.279 1.640 -1.440 5 A_DC5:DG16_B A 5 ? B 16 ? 19 1 1 A DA 7 1_555 B DT 4 1_555 0.239 0.027 0.333 1.776 -3.931 3.513 6 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DT 8 1_555 B DA 3 1_555 0.021 -0.113 -0.121 2.900 -5.532 -0.876 7 A_DT8:DA13_B A 8 ? B 13 ? 20 1 1 A DC 9 1_555 B DG 2 1_555 0.276 -0.208 -0.127 -1.107 -3.330 -3.174 8 A_DC9:DG12_B A 9 ? B 12 ? 19 1 1 A DT 10 1_555 B DA 1 1_555 0.047 -0.078 -0.151 -10.712 -11.834 8.016 9 A_DT10:DA11_B A 10 ? B 11 ? 20 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 DA 1 1_555 B DT 10 1_555 A DC 2 1_555 B DG 9 1_555 0.156 -0.565 3.809 3.108 -2.174 35.164 -0.554 0.280 3.835 -3.586 -5.126 35.361 1 AA_DA1DC2:DG19DT20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DA 3 1_555 B DT 8 1_555 -0.417 -0.724 3.608 0.101 6.981 39.986 -1.889 0.614 3.438 10.115 -0.146 40.566 2 AA_DC2DA3:DT18DG19_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 0.176 -0.511 3.276 -0.707 -2.651 31.236 -0.442 -0.460 3.303 -4.911 1.311 31.353 3 AA_DA3DT4:DA17DT18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DC 5 1_555 B DG 6 1_555 0.206 -0.287 3.079 -1.136 0.580 35.812 -0.544 -0.487 3.066 0.942 1.846 35.834 4 AA_DT4DC5:DG16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 7 1_555 B DT 4 1_555 A DT 8 1_555 B DA 3 1_555 -0.542 -0.809 3.334 3.097 -4.900 28.073 -0.492 1.818 3.346 -9.967 -6.300 28.653 5 AA_DA7DT8:DA13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DT 8 1_555 B DA 3 1_555 A DC 9 1_555 B DG 2 1_555 -0.067 -0.800 3.404 -2.193 0.507 38.970 -1.260 -0.175 3.392 0.760 3.284 39.033 6 AA_DT8DC9:DG12DA13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DC 9 1_555 B DG 2 1_555 A DT 10 1_555 B DA 1 1_555 1.115 -0.830 3.465 4.182 5.281 28.271 -2.888 -1.246 3.384 10.621 -8.412 29.047 7 AA_DC9DT10:DA11DG12_BB A 9 ? B 12 ? A 10 ? B 11 ? # 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 DRX 500 2 ? Bruker DRX 800 3 ? Bruker DRX 600 # _atom_sites.entry_id 1MK6 _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_