data_1M6F # _entry.id 1M6F # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 1M6F pdb_00001m6f 10.2210/pdb1m6f/pdb NDB DD0052 ? ? RCSB RCSB016655 ? ? WWPDB D_1000016655 ? ? # 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 2002-11-15 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 2024-04-03 # _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' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Structure summary' 8 6 'Structure model' 'Refinement description' # 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' software 2 5 'Structure model' chem_comp 3 5 'Structure model' chem_comp_atom 4 5 'Structure model' chem_comp_bond 5 5 'Structure model' database_2 6 5 'Structure model' pdbx_struct_conn_angle 7 5 'Structure model' struct_conn 8 5 'Structure model' struct_site 9 6 'Structure model' pdbx_initial_refinement_model # 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 5 'Structure model' '_chem_comp.pdbx_synonyms' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.value' 11 5 'Structure model' '_struct_conn.pdbx_dist_value' 12 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1M6F _pdbx_database_status.recvd_initial_deposition_date 2002-07-16 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nguyen, B.' 1 'Lee, M.P.H.' 2 'Hamelberg, D.' 3 'Joubert, A.' 4 'Bailly, C.' 5 'Brun, R.' 6 'Neidle, S.' 7 'Wilson, W.D.' 8 # _citation.id primary _citation.title 'Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 124 _citation.page_first 13680 _citation.page_last 13681 _citation.year 2002 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12431090 _citation.pdbx_database_id_DOI 10.1021/ja027953c # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nguyen, B.' 1 ? primary 'Lee, M.P.H.' 2 ? primary 'Hamelberg, D.' 3 ? primary 'Joubert, A.' 4 ? primary 'Bailly, C.' 5 ? primary 'Brun, R.' 6 ? primary 'Neidle, S.' 7 ? primary 'Wilson, W.D.' 8 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') ; 3663.392 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn "3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM" 352.417 1 ? ? ? ? 4 water nat water 18.015 117 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 "3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM" CGQ 4 water HOH # 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 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG n # 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 CGQ non-polymer . "3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM" 'CGP40215A; BIS[[3-(AMINOIMINOMETHYL)PHENYL]METHYLENE] CARBONIMIDIC DIHYDRAZIDE' 'C17 H22 N9 3' 352.417 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 1001 1001 DC C A . n A 1 2 DG 2 1002 1002 DG G A . n A 1 3 DC 3 1003 1003 DC C A . n A 1 4 DG 4 1004 1004 DG G A . n A 1 5 DA 5 1005 1005 DA A A . n A 1 6 DA 6 1006 1006 DA A A . n A 1 7 DT 7 1007 1007 DT T A . n A 1 8 DT 8 1008 1008 DT T A . n A 1 9 DC 9 1009 1009 DC C A . n A 1 10 DG 10 1010 1010 DG G A . n A 1 11 DC 11 1011 1011 DC C A . n A 1 12 DG 12 1012 1012 DG G A . n B 1 1 DC 1 2013 2013 DC C B . n B 1 2 DG 2 2014 2014 DG G B . n B 1 3 DC 3 2015 2015 DC C B . n B 1 4 DG 4 2016 2016 DG G B . n B 1 5 DA 5 2017 2017 DA A B . n B 1 6 DA 6 2018 2018 DA A B . n B 1 7 DT 7 2019 2019 DT T B . n B 1 8 DT 8 2020 2020 DT T B . n B 1 9 DC 9 2021 2021 DC C B . n B 1 10 DG 10 2022 2022 DG G B . n B 1 11 DC 11 2023 2023 DC C B . n B 1 12 DG 12 2024 2024 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MG 1 4026 4026 MG MO6 A . D 3 CGQ 1 3025 3025 CGQ CGQ B . E 4 HOH 1 8002 8002 HOH HOH A . E 4 HOH 2 8004 8004 HOH HOH A . E 4 HOH 3 8009 8009 HOH HOH A . E 4 HOH 4 8010 8010 HOH HOH A . E 4 HOH 5 8011 8011 HOH HOH A . E 4 HOH 6 8013 8013 HOH HOH A . E 4 HOH 7 8014 8014 HOH HOH A . E 4 HOH 8 8016 8016 HOH HOH A . E 4 HOH 9 8018 8018 HOH HOH A . E 4 HOH 10 8019 8019 HOH HOH A . E 4 HOH 11 8020 8020 HOH HOH A . E 4 HOH 12 8021 8021 HOH HOH A . E 4 HOH 13 8022 8022 HOH HOH A . E 4 HOH 14 8025 8025 HOH HOH A . E 4 HOH 15 8028 8028 HOH HOH A . E 4 HOH 16 8031 8031 HOH HOH A . E 4 HOH 17 8032 8032 HOH HOH A . E 4 HOH 18 8034 8034 HOH HOH A . E 4 HOH 19 8035 8035 HOH HOH A . E 4 HOH 20 8036 8036 HOH HOH A . E 4 HOH 21 8037 8037 HOH HOH A . E 4 HOH 22 8038 8038 HOH HOH A . E 4 HOH 23 8039 8039 HOH HOH A . E 4 HOH 24 8040 8040 HOH HOH A . E 4 HOH 25 8041 8041 HOH HOH A . E 4 HOH 26 8044 8044 HOH HOH A . E 4 HOH 27 8051 8051 HOH HOH A . E 4 HOH 28 8054 8054 HOH HOH A . E 4 HOH 29 8056 8056 HOH HOH A . E 4 HOH 30 8057 8057 HOH HOH A . E 4 HOH 31 8058 8058 HOH HOH A . E 4 HOH 32 8059 8059 HOH HOH A . E 4 HOH 33 8060 8060 HOH HOH A . E 4 HOH 34 8065 8065 HOH HOH A . E 4 HOH 35 8067 8067 HOH HOH A . E 4 HOH 36 8068 8068 HOH HOH A . E 4 HOH 37 8071 8071 HOH HOH A . E 4 HOH 38 8075 8075 HOH HOH A . E 4 HOH 39 8078 8078 HOH HOH A . E 4 HOH 40 8084 8084 HOH HOH A . E 4 HOH 41 8085 8085 HOH HOH A . E 4 HOH 42 8086 8086 HOH HOH A . E 4 HOH 43 8087 8087 HOH HOH A . E 4 HOH 44 8088 8088 HOH HOH A . E 4 HOH 45 8090 8090 HOH HOH A . E 4 HOH 46 8091 8091 HOH HOH A . E 4 HOH 47 8094 8094 HOH HOH A . E 4 HOH 48 8095 8095 HOH HOH A . E 4 HOH 49 8096 8096 HOH HOH A . E 4 HOH 50 8097 8097 HOH HOH A . E 4 HOH 51 8100 8100 HOH HOH A . E 4 HOH 52 8101 8101 HOH HOH A . E 4 HOH 53 8102 8102 HOH HOH A . E 4 HOH 54 8105 8105 HOH HOH A . E 4 HOH 55 8109 8109 HOH HOH A . E 4 HOH 56 8110 8110 HOH HOH A . E 4 HOH 57 8111 8111 HOH HOH A . E 4 HOH 58 8113 4026 HOH MO6 A . E 4 HOH 59 8114 4026 HOH MO6 A . E 4 HOH 60 8115 4026 HOH MO6 A . E 4 HOH 61 8116 4026 HOH MO6 A . E 4 HOH 62 8117 4026 HOH MO6 A . F 4 HOH 1 8001 8001 HOH HOH B . F 4 HOH 2 8003 8003 HOH HOH B . F 4 HOH 3 8005 8005 HOH HOH B . F 4 HOH 4 8006 8006 HOH HOH B . F 4 HOH 5 8007 8007 HOH HOH B . F 4 HOH 6 8008 8008 HOH HOH B . F 4 HOH 7 8012 8012 HOH HOH B . F 4 HOH 8 8015 8015 HOH HOH B . F 4 HOH 9 8017 8017 HOH HOH B . F 4 HOH 10 8023 8023 HOH HOH B . F 4 HOH 11 8024 8024 HOH HOH B . F 4 HOH 12 8026 8026 HOH HOH B . F 4 HOH 13 8027 8027 HOH HOH B . F 4 HOH 14 8029 8029 HOH HOH B . F 4 HOH 15 8030 8030 HOH HOH B . F 4 HOH 16 8033 8033 HOH HOH B . F 4 HOH 17 8042 8042 HOH HOH B . F 4 HOH 18 8043 8043 HOH HOH B . F 4 HOH 19 8045 8045 HOH HOH B . F 4 HOH 20 8046 8046 HOH HOH B . F 4 HOH 21 8047 8047 HOH HOH B . F 4 HOH 22 8048 8048 HOH HOH B . F 4 HOH 23 8049 8049 HOH HOH B . F 4 HOH 24 8050 8050 HOH HOH B . F 4 HOH 25 8052 8052 HOH HOH B . F 4 HOH 26 8053 8053 HOH HOH B . F 4 HOH 27 8055 8055 HOH HOH B . F 4 HOH 28 8061 8061 HOH HOH B . F 4 HOH 29 8062 8062 HOH HOH B . F 4 HOH 30 8063 8063 HOH HOH B . F 4 HOH 31 8064 8064 HOH HOH B . F 4 HOH 32 8066 8066 HOH HOH B . F 4 HOH 33 8069 8069 HOH HOH B . F 4 HOH 34 8070 8070 HOH HOH B . F 4 HOH 35 8072 8072 HOH HOH B . F 4 HOH 36 8073 8073 HOH HOH B . F 4 HOH 37 8074 8074 HOH HOH B . F 4 HOH 38 8076 8076 HOH HOH B . F 4 HOH 39 8077 8077 HOH HOH B . F 4 HOH 40 8079 8079 HOH HOH B . F 4 HOH 41 8080 8080 HOH HOH B . F 4 HOH 42 8081 8081 HOH HOH B . F 4 HOH 43 8082 8082 HOH HOH B . F 4 HOH 44 8083 8083 HOH HOH B . F 4 HOH 45 8089 8089 HOH HOH B . F 4 HOH 46 8092 8092 HOH HOH B . F 4 HOH 47 8093 8093 HOH HOH B . F 4 HOH 48 8098 8098 HOH HOH B . F 4 HOH 49 8099 8099 HOH HOH B . F 4 HOH 50 8103 8103 HOH HOH B . F 4 HOH 51 8104 8104 HOH HOH B . F 4 HOH 52 8106 8106 HOH HOH B . F 4 HOH 53 8107 8107 HOH HOH B . F 4 HOH 54 8108 8108 HOH HOH B . F 4 HOH 55 8112 4026 HOH MO6 B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SCALEPACK 'data scaling' . ? 1 X-PLOR 'model building' . ? 2 SHELXL-97 refinement . ? 3 X-PLOR phasing . ? 4 # _cell.entry_id 1M6F _cell.length_a 24.098 _cell.length_b 39.821 _cell.length_c 65.620 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1M6F _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _exptl.entry_id 1M6F _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 40.25 _exptl_crystal.density_Matthews 2.06 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 285 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details ;MGCL2 2UL OF 75MM, DNA DOUBLE-STRANDED 3UL OF 2MM, MPD 2UL OF 25%, DRUG 2UL OF 4.5MM, SODIUM CACODYLATE 40MM. MPD IN RESERVOIR 700UL OF 50%., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 MGCL2 ? ? ? 1 2 1 DNA ? ? ? 1 3 1 MPD ? ? ? 1 4 1 DRUG ? ? ? 1 5 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 104 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2002-06-27 _diffrn_detector.details 'Yale Focussing Mirrors' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 1M6F _reflns.observed_criterion_sigma_F 1 _reflns.observed_criterion_sigma_I 1 _reflns.d_resolution_high 1.78 _reflns.d_resolution_low 17.00 _reflns.number_all ? _reflns.number_obs 6040 _reflns.percent_possible_obs 92.8 _reflns.pdbx_Rmerge_I_obs 0.047 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.8 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.78 _reflns_shell.d_res_low 1.84 _reflns_shell.percent_possible_obs 90.6 _reflns_shell.percent_possible_all 90.6 _reflns_shell.Rmerge_I_obs 0.184 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_redundancy ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1M6F _refine.ls_d_res_high 1.78 _refine.ls_d_res_low 10.00 _refine.pdbx_ls_sigma_F 4 _refine.pdbx_ls_sigma_I 2 _refine.ls_number_reflns_all 5636 _refine.ls_number_reflns_obs 5477 _refine.ls_number_reflns_R_free 298 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.205 _refine.ls_R_factor_R_work 0.202 _refine.ls_R_factor_R_free 0.277 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'DNA PART OF NDB ENTRY GDL009' _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 486 _refine_hist.pdbx_number_atoms_ligand 42 _refine_hist.number_atoms_solvent 111 _refine_hist.number_atoms_total 639 _refine_hist.d_res_high 1.78 _refine_hist.d_res_low 10.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.020 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.019 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.006 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.010 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1M6F _pdbx_refine.R_factor_all_no_cutoff 0.205 _pdbx_refine.R_factor_obs_no_cutoff 0.202 _pdbx_refine.number_reflns_obs_no_cutoff 5636 _pdbx_refine.free_R_factor_no_cutoff 0.277 _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff 0.202 _pdbx_refine.R_factor_obs_4sig_cutoff 0.199 _pdbx_refine.number_reflns_obs_4sig_cutoff 5477 _pdbx_refine.free_R_factor_4sig_cutoff 0.271 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 289 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1M6F _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 1M6F _struct.title 'Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1M6F _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Nucleic acids, minor groove binder, double helix, DNA-drug 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 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1M6F _struct_ref.pdbx_db_accession 1M6F _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1M6F A 1 ? 12 ? 1M6F 1001 ? 1012 ? 1001 1012 2 1 1M6F B 1 ? 12 ? 1M6F 2013 ? 2024 ? 2013 2024 # _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,D,E,F # _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 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # 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 metalc1 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 4026 A HOH 8113 1_555 ? ? ? ? ? ? ? 2.011 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 4026 A HOH 8114 1_555 ? ? ? ? ? ? ? 2.031 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 4026 A HOH 8115 1_555 ? ? ? ? ? ? ? 2.019 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 4026 A HOH 8116 1_555 ? ? ? ? ? ? ? 2.023 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 4026 A HOH 8117 1_555 ? ? ? ? ? ? ? 2.024 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 4026 B HOH 8112 1_555 ? ? ? ? ? ? ? 2.019 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1001 B DG 2024 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1001 B DG 2024 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1001 B DG 2024 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 1002 B DC 2023 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 1002 B DC 2023 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 1002 B DC 2023 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1003 B DG 2022 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1003 B DG 2022 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1003 B DG 2022 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 1004 B DC 2021 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 1004 B DC 2021 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 1004 B DC 2021 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 1005 B DT 2020 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 1005 B DT 2020 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 1006 B DT 2019 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 1006 B DT 2019 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 1007 B DA 2018 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 1007 B DA 2018 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 1008 B DA 2017 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 1008 B DA 2017 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 1009 B DG 2016 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 1009 B DG 2016 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 1009 B DG 2016 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 1010 B DC 2015 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 1010 B DC 2015 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 1010 B DC 2015 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 1011 B DG 2014 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 1011 B DG 2014 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 1011 B DG 2014 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 1012 B DC 2013 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 1012 B DC 2013 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 1012 B DC 2013 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 8113 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8114 ? 1_555 88.7 ? 2 O ? E HOH . ? A HOH 8113 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8115 ? 1_555 176.6 ? 3 O ? E HOH . ? A HOH 8114 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8115 ? 1_555 88.7 ? 4 O ? E HOH . ? A HOH 8113 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8116 ? 1_555 90.6 ? 5 O ? E HOH . ? A HOH 8114 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8116 ? 1_555 90.5 ? 6 O ? E HOH . ? A HOH 8115 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8116 ? 1_555 91.5 ? 7 O ? E HOH . ? A HOH 8113 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8117 ? 1_555 90.9 ? 8 O ? E HOH . ? A HOH 8114 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8117 ? 1_555 91.4 ? 9 O ? E HOH . ? A HOH 8115 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8117 ? 1_555 87.1 ? 10 O ? E HOH . ? A HOH 8116 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? E HOH . ? A HOH 8117 ? 1_555 177.6 ? 11 O ? E HOH . ? A HOH 8113 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? F HOH . ? B HOH 8112 ? 1_555 91.0 ? 12 O ? E HOH . ? A HOH 8114 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? F HOH . ? B HOH 8112 ? 1_555 179.6 ? 13 O ? E HOH . ? A HOH 8115 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? F HOH . ? B HOH 8112 ? 1_555 91.7 ? 14 O ? E HOH . ? A HOH 8116 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? F HOH . ? B HOH 8112 ? 1_555 89.6 ? 15 O ? E HOH . ? A HOH 8117 ? 1_555 MG ? C MG . ? A MG 4026 ? 1_555 O ? F HOH . ? B HOH 8112 ? 1_555 88.5 ? # 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 B CGQ 3025 ? 14 'BINDING SITE FOR RESIDUE CGQ B 3025' AC2 Software A MG 4026 ? 6 'BINDING SITE FOR RESIDUE MG A 4026' 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 14 DG A 4 ? DG A 1004 . ? 1_455 ? 2 AC1 14 DA A 6 ? DA A 1006 . ? 1_555 ? 3 AC1 14 DT A 7 ? DT A 1007 . ? 1_555 ? 4 AC1 14 DT A 8 ? DT A 1008 . ? 1_555 ? 5 AC1 14 DC A 9 ? DC A 1009 . ? 1_555 ? 6 AC1 14 DA B 6 ? DA B 2018 . ? 1_555 ? 7 AC1 14 DT B 7 ? DT B 2019 . ? 1_555 ? 8 AC1 14 DT B 8 ? DT B 2020 . ? 1_555 ? 9 AC1 14 DC B 9 ? DC B 2021 . ? 1_555 ? 10 AC1 14 HOH F . ? HOH B 8017 . ? 1_555 ? 11 AC1 14 HOH F . ? HOH B 8030 . ? 1_555 ? 12 AC1 14 HOH F . ? HOH B 8033 . ? 1_555 ? 13 AC1 14 HOH F . ? HOH B 8045 . ? 1_555 ? 14 AC1 14 HOH F . ? HOH B 8099 . ? 1_555 ? 15 AC2 6 HOH E . ? HOH A 8113 . ? 1_555 ? 16 AC2 6 HOH E . ? HOH A 8114 . ? 1_555 ? 17 AC2 6 HOH E . ? HOH A 8115 . ? 1_555 ? 18 AC2 6 HOH E . ? HOH A 8116 . ? 1_555 ? 19 AC2 6 HOH E . ? HOH A 8117 . ? 1_555 ? 20 AC2 6 HOH F . ? HOH B 8112 . ? 1_555 ? # 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 "O4'" A DC 1001 ? ? "C1'" A DC 1001 ? ? N1 A DC 1001 ? ? 101.14 108.00 -6.86 0.70 N 2 1 "C3'" A DG 1002 ? ? "O3'" A DG 1002 ? ? P A DC 1003 ? ? 126.96 119.70 7.26 1.20 Y 3 1 "O4'" A DC 1003 ? ? "C1'" A DC 1003 ? ? N1 A DC 1003 ? ? 102.61 108.00 -5.39 0.70 N 4 1 "O4'" A DA 1005 ? ? "C1'" A DA 1005 ? ? N9 A DA 1005 ? ? 100.06 108.00 -7.94 0.70 N 5 1 "O4'" A DA 1006 ? ? "C1'" A DA 1006 ? ? N9 A DA 1006 ? ? 99.52 108.00 -8.48 0.70 N 6 1 N1 A DT 1007 ? ? "C1'" A DT 1007 ? ? "C2'" A DT 1007 ? ? 123.96 114.30 9.66 1.40 N 7 1 "O4'" A DT 1007 ? ? "C1'" A DT 1007 ? ? N1 A DT 1007 ? ? 98.73 108.00 -9.27 0.70 N 8 1 N1 A DT 1008 ? ? "C1'" A DT 1008 ? ? "C2'" A DT 1008 ? ? 123.15 114.30 8.85 1.40 N 9 1 "O4'" A DT 1008 ? ? "C1'" A DT 1008 ? ? N1 A DT 1008 ? ? 99.96 108.00 -8.04 0.70 N 10 1 "O4'" A DC 1009 ? ? "C1'" A DC 1009 ? ? N1 A DC 1009 ? ? 101.97 108.00 -6.03 0.70 N 11 1 "O4'" A DC 1011 ? ? "C1'" A DC 1011 ? ? N1 A DC 1011 ? ? 99.01 108.00 -8.99 0.70 N 12 1 "O4'" B DC 2015 ? ? "C1'" B DC 2015 ? ? N1 B DC 2015 ? ? 100.82 108.00 -7.18 0.70 N 13 1 "O4'" B DG 2016 ? ? "C1'" B DG 2016 ? ? N9 B DG 2016 ? ? 103.36 108.00 -4.64 0.70 N 14 1 "O4'" B DA 2017 ? ? "C1'" B DA 2017 ? ? N9 B DA 2017 ? ? 96.79 108.00 -11.21 0.70 N 15 1 N9 B DA 2018 ? ? "C1'" B DA 2018 ? ? "C2'" B DA 2018 ? ? 123.65 114.30 9.35 1.40 N 16 1 "O4'" B DA 2018 ? ? "C1'" B DA 2018 ? ? N9 B DA 2018 ? ? 95.92 108.00 -12.08 0.70 N 17 1 "O4'" B DT 2019 ? ? "C1'" B DT 2019 ? ? N1 B DT 2019 ? ? 103.23 108.00 -4.77 0.70 N 18 1 N1 B DT 2020 ? ? "C1'" B DT 2020 ? ? "C2'" B DT 2020 ? ? 123.88 114.30 9.58 1.40 N 19 1 "O4'" B DT 2020 ? ? "C1'" B DT 2020 ? ? N1 B DT 2020 ? ? 98.36 108.00 -9.64 0.70 N 20 1 N3 B DT 2020 ? ? C4 B DT 2020 ? ? O4 B DT 2020 ? ? 123.91 119.90 4.01 0.60 N 21 1 N1 B DC 2021 ? ? "C1'" B DC 2021 ? ? "C2'" B DC 2021 ? ? 122.84 114.30 8.54 1.40 N 22 1 "O4'" B DC 2021 ? ? "C1'" B DC 2021 ? ? N1 B DC 2021 ? ? 96.65 108.00 -11.35 0.70 N 23 1 "C3'" B DG 2022 ? ? "C2'" B DG 2022 ? ? "C1'" B DG 2022 ? ? 97.59 102.40 -4.81 0.80 N 24 1 "O4'" B DG 2024 ? ? "C1'" B DG 2024 ? ? N9 B DG 2024 ? ? 103.70 108.00 -4.30 0.70 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # 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 CGQ C1 C Y N 1 CGQ C2 C Y N 2 CGQ C3 C Y N 3 CGQ C4 C Y N 4 CGQ C5 C Y N 5 CGQ C6 C Y N 6 CGQ C7 C N N 7 CGQ N8 N N N 8 CGQ C9 C N N 9 CGQ N10 N N N 10 CGQ N11 N N N 11 CGQ N12 N N N 12 CGQ C13 C N N 13 CGQ N15 N N N 14 CGQ N19 N N N 15 CGQ N20 N N N 16 CGQ C21 C N N 17 CGQ C22 C Y N 18 CGQ C23 C Y N 19 CGQ C24 C Y N 20 CGQ C25 C Y N 21 CGQ C26 C Y N 22 CGQ C27 C Y N 23 CGQ C28 C N N 24 CGQ N29 N N N 25 CGQ N30 N N N 26 CGQ H21 H N N 27 CGQ H41 H N N 28 CGQ H51 H N N 29 CGQ H61 H N N 30 CGQ H71 H N N 31 CGQ H101 H N N 32 CGQ H102 H N N 33 CGQ H111 H N N 34 CGQ H112 H N N 35 CGQ H121 H N N 36 CGQ H151 H N N 37 CGQ H152 H N N 38 CGQ H191 H N N 39 CGQ H211 H N N 40 CGQ H231 H N N 41 CGQ H241 H N N 42 CGQ H251 H N N 43 CGQ H271 H N N 44 CGQ H291 H N N 45 CGQ H292 H N N 46 CGQ H301 H N N 47 CGQ H302 H N N 48 DA OP3 O N N 49 DA P P N N 50 DA OP1 O N N 51 DA OP2 O N N 52 DA "O5'" O N N 53 DA "C5'" C N N 54 DA "C4'" C N R 55 DA "O4'" O N N 56 DA "C3'" C N S 57 DA "O3'" O N N 58 DA "C2'" C N N 59 DA "C1'" C N R 60 DA N9 N Y N 61 DA C8 C Y N 62 DA N7 N Y N 63 DA C5 C Y N 64 DA C6 C Y N 65 DA N6 N N N 66 DA N1 N Y N 67 DA C2 C Y N 68 DA N3 N Y N 69 DA C4 C Y N 70 DA HOP3 H N N 71 DA HOP2 H N N 72 DA "H5'" H N N 73 DA "H5''" H N N 74 DA "H4'" H N N 75 DA "H3'" H N N 76 DA "HO3'" H N N 77 DA "H2'" H N N 78 DA "H2''" H N N 79 DA "H1'" H N N 80 DA H8 H N N 81 DA H61 H N N 82 DA H62 H N N 83 DA H2 H N N 84 DC OP3 O N N 85 DC P P N N 86 DC OP1 O N N 87 DC OP2 O N N 88 DC "O5'" O N N 89 DC "C5'" C N N 90 DC "C4'" C N R 91 DC "O4'" O N N 92 DC "C3'" C N S 93 DC "O3'" O N N 94 DC "C2'" C N N 95 DC "C1'" C N R 96 DC N1 N N N 97 DC C2 C N N 98 DC O2 O N N 99 DC N3 N N N 100 DC C4 C N N 101 DC N4 N N N 102 DC C5 C N N 103 DC C6 C N N 104 DC HOP3 H N N 105 DC HOP2 H N N 106 DC "H5'" H N N 107 DC "H5''" H N N 108 DC "H4'" H N N 109 DC "H3'" H N N 110 DC "HO3'" H N N 111 DC "H2'" H N N 112 DC "H2''" H N N 113 DC "H1'" H N N 114 DC H41 H N N 115 DC H42 H N N 116 DC H5 H N N 117 DC H6 H N N 118 DG OP3 O N N 119 DG P P N N 120 DG OP1 O N N 121 DG OP2 O N N 122 DG "O5'" O N N 123 DG "C5'" C N N 124 DG "C4'" C N R 125 DG "O4'" O N N 126 DG "C3'" C N S 127 DG "O3'" O N N 128 DG "C2'" C N N 129 DG "C1'" C N R 130 DG N9 N Y N 131 DG C8 C Y N 132 DG N7 N Y N 133 DG C5 C Y N 134 DG C6 C N N 135 DG O6 O N N 136 DG N1 N N N 137 DG C2 C N N 138 DG N2 N N N 139 DG N3 N N N 140 DG C4 C Y N 141 DG HOP3 H N N 142 DG HOP2 H N N 143 DG "H5'" H N N 144 DG "H5''" H N N 145 DG "H4'" H N N 146 DG "H3'" H N N 147 DG "HO3'" H N N 148 DG "H2'" H N N 149 DG "H2''" H N N 150 DG "H1'" H N N 151 DG H8 H N N 152 DG H1 H N N 153 DG H21 H N N 154 DG H22 H N N 155 DT OP3 O N N 156 DT P P N N 157 DT OP1 O N N 158 DT OP2 O N N 159 DT "O5'" O N N 160 DT "C5'" C N N 161 DT "C4'" C N R 162 DT "O4'" O N N 163 DT "C3'" C N S 164 DT "O3'" O N N 165 DT "C2'" C N N 166 DT "C1'" C N R 167 DT N1 N N N 168 DT C2 C N N 169 DT O2 O N N 170 DT N3 N N N 171 DT C4 C N N 172 DT O4 O N N 173 DT C5 C N N 174 DT C7 C N N 175 DT C6 C N N 176 DT HOP3 H N N 177 DT HOP2 H N N 178 DT "H5'" H N N 179 DT "H5''" H N N 180 DT "H4'" H N N 181 DT "H3'" H N N 182 DT "HO3'" H N N 183 DT "H2'" H N N 184 DT "H2''" H N N 185 DT "H1'" H N N 186 DT H3 H N N 187 DT H71 H N N 188 DT H72 H N N 189 DT H73 H N N 190 DT H6 H N N 191 HOH O O N N 192 HOH H1 H N N 193 HOH H2 H N N 194 MG MG MG N N 195 # 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 CGQ C1 C2 doub Y N 1 CGQ C1 C6 sing Y N 2 CGQ C1 C9 sing N N 3 CGQ C2 C3 sing Y N 4 CGQ C2 H21 sing N N 5 CGQ C3 C4 doub Y N 6 CGQ C3 C7 sing N N 7 CGQ C4 C5 sing Y N 8 CGQ C4 H41 sing N N 9 CGQ C5 C6 doub Y N 10 CGQ C5 H51 sing N N 11 CGQ C6 H61 sing N N 12 CGQ C7 N8 doub N E 13 CGQ C7 H71 sing N N 14 CGQ N8 N12 sing N N 15 CGQ C9 N10 doub N N 16 CGQ C9 N11 sing N N 17 CGQ N10 H101 sing N N 18 CGQ N10 H102 sing N N 19 CGQ N11 H111 sing N N 20 CGQ N11 H112 sing N N 21 CGQ N12 C13 sing N N 22 CGQ N12 H121 sing N N 23 CGQ C13 N15 sing N N 24 CGQ C13 N19 doub N E 25 CGQ N15 H151 sing N N 26 CGQ N15 H152 sing N N 27 CGQ N19 N20 sing N N 28 CGQ N19 H191 sing N N 29 CGQ N20 C21 doub N N 30 CGQ C21 C22 sing N N 31 CGQ C21 H211 sing N N 32 CGQ C22 C23 doub Y N 33 CGQ C22 C27 sing Y N 34 CGQ C23 C24 sing Y N 35 CGQ C23 H231 sing N N 36 CGQ C24 C25 doub Y N 37 CGQ C24 H241 sing N N 38 CGQ C25 C26 sing Y N 39 CGQ C25 H251 sing N N 40 CGQ C26 C27 doub Y N 41 CGQ C26 C28 sing N N 42 CGQ C27 H271 sing N N 43 CGQ C28 N29 doub N N 44 CGQ C28 N30 sing N N 45 CGQ N29 H291 sing N N 46 CGQ N29 H292 sing N N 47 CGQ N30 H301 sing N N 48 CGQ N30 H302 sing N N 49 DA OP3 P sing N N 50 DA OP3 HOP3 sing N N 51 DA P OP1 doub N N 52 DA P OP2 sing N N 53 DA P "O5'" sing N N 54 DA OP2 HOP2 sing N N 55 DA "O5'" "C5'" sing N N 56 DA "C5'" "C4'" sing N N 57 DA "C5'" "H5'" sing N N 58 DA "C5'" "H5''" sing N N 59 DA "C4'" "O4'" sing N N 60 DA "C4'" "C3'" sing N N 61 DA "C4'" "H4'" sing N N 62 DA "O4'" "C1'" sing N N 63 DA "C3'" "O3'" sing N N 64 DA "C3'" "C2'" sing N N 65 DA "C3'" "H3'" sing N N 66 DA "O3'" "HO3'" sing N N 67 DA "C2'" "C1'" sing N N 68 DA "C2'" "H2'" sing N N 69 DA "C2'" "H2''" sing N N 70 DA "C1'" N9 sing N N 71 DA "C1'" "H1'" sing N N 72 DA N9 C8 sing Y N 73 DA N9 C4 sing Y N 74 DA C8 N7 doub Y N 75 DA C8 H8 sing N N 76 DA N7 C5 sing Y N 77 DA C5 C6 sing Y N 78 DA C5 C4 doub Y N 79 DA C6 N6 sing N N 80 DA C6 N1 doub Y N 81 DA N6 H61 sing N N 82 DA N6 H62 sing N N 83 DA N1 C2 sing Y N 84 DA C2 N3 doub Y N 85 DA C2 H2 sing N N 86 DA N3 C4 sing Y N 87 DC OP3 P sing N N 88 DC OP3 HOP3 sing N N 89 DC P OP1 doub N N 90 DC P OP2 sing N N 91 DC P "O5'" sing N N 92 DC OP2 HOP2 sing N N 93 DC "O5'" "C5'" sing N N 94 DC "C5'" "C4'" sing N N 95 DC "C5'" "H5'" sing N N 96 DC "C5'" "H5''" sing N N 97 DC "C4'" "O4'" sing N N 98 DC "C4'" "C3'" sing N N 99 DC "C4'" "H4'" sing N N 100 DC "O4'" "C1'" sing N N 101 DC "C3'" "O3'" sing N N 102 DC "C3'" "C2'" sing N N 103 DC "C3'" "H3'" sing N N 104 DC "O3'" "HO3'" sing N N 105 DC "C2'" "C1'" sing N N 106 DC "C2'" "H2'" sing N N 107 DC "C2'" "H2''" sing N N 108 DC "C1'" N1 sing N N 109 DC "C1'" "H1'" sing N N 110 DC N1 C2 sing N N 111 DC N1 C6 sing N N 112 DC C2 O2 doub N N 113 DC C2 N3 sing N N 114 DC N3 C4 doub N N 115 DC C4 N4 sing N N 116 DC C4 C5 sing N N 117 DC N4 H41 sing N N 118 DC N4 H42 sing N N 119 DC C5 C6 doub N N 120 DC C5 H5 sing N N 121 DC C6 H6 sing N N 122 DG OP3 P sing N N 123 DG OP3 HOP3 sing N N 124 DG P OP1 doub N N 125 DG P OP2 sing N N 126 DG P "O5'" sing N N 127 DG OP2 HOP2 sing N N 128 DG "O5'" "C5'" sing N N 129 DG "C5'" "C4'" sing N N 130 DG "C5'" "H5'" sing N N 131 DG "C5'" "H5''" sing N N 132 DG "C4'" "O4'" sing N N 133 DG "C4'" "C3'" sing N N 134 DG "C4'" "H4'" sing N N 135 DG "O4'" "C1'" sing N N 136 DG "C3'" "O3'" sing N N 137 DG "C3'" "C2'" sing N N 138 DG "C3'" "H3'" sing N N 139 DG "O3'" "HO3'" sing N N 140 DG "C2'" "C1'" sing N N 141 DG "C2'" "H2'" sing N N 142 DG "C2'" "H2''" sing N N 143 DG "C1'" N9 sing N N 144 DG "C1'" "H1'" sing N N 145 DG N9 C8 sing Y N 146 DG N9 C4 sing Y N 147 DG C8 N7 doub Y N 148 DG C8 H8 sing N N 149 DG N7 C5 sing Y N 150 DG C5 C6 sing N N 151 DG C5 C4 doub Y N 152 DG C6 O6 doub N N 153 DG C6 N1 sing N N 154 DG N1 C2 sing N N 155 DG N1 H1 sing N N 156 DG C2 N2 sing N N 157 DG C2 N3 doub N N 158 DG N2 H21 sing N N 159 DG N2 H22 sing N N 160 DG N3 C4 sing N N 161 DT OP3 P sing N N 162 DT OP3 HOP3 sing N N 163 DT P OP1 doub N N 164 DT P OP2 sing N N 165 DT P "O5'" sing N N 166 DT OP2 HOP2 sing N N 167 DT "O5'" "C5'" sing N N 168 DT "C5'" "C4'" sing N N 169 DT "C5'" "H5'" sing N N 170 DT "C5'" "H5''" sing N N 171 DT "C4'" "O4'" sing N N 172 DT "C4'" "C3'" sing N N 173 DT "C4'" "H4'" sing N N 174 DT "O4'" "C1'" sing N N 175 DT "C3'" "O3'" sing N N 176 DT "C3'" "C2'" sing N N 177 DT "C3'" "H3'" sing N N 178 DT "O3'" "HO3'" sing N N 179 DT "C2'" "C1'" sing N N 180 DT "C2'" "H2'" sing N N 181 DT "C2'" "H2''" sing N N 182 DT "C1'" N1 sing N N 183 DT "C1'" "H1'" sing N N 184 DT N1 C2 sing N N 185 DT N1 C6 sing N N 186 DT C2 O2 doub N N 187 DT C2 N3 sing N N 188 DT N3 C4 sing N N 189 DT N3 H3 sing N N 190 DT C4 O4 doub N N 191 DT C4 C5 sing N N 192 DT C5 C7 sing N N 193 DT C5 C6 doub N N 194 DT C7 H71 sing N N 195 DT C7 H72 sing N N 196 DT C7 H73 sing N N 197 DT C6 H6 sing N N 198 HOH O H1 sing N N 199 HOH O H2 sing N N 200 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1M6F 'double helix' 1M6F '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 DC 1 1_555 B DG 12 1_555 0.289 -0.123 0.021 3.244 -21.070 1.610 1 A_DC1001:DG2024_B A 1001 ? B 2024 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.076 -0.124 0.050 -2.095 -3.969 -3.862 2 A_DG1002:DC2023_B A 1002 ? B 2023 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.179 -0.158 0.245 -2.376 -4.947 0.609 3 A_DC1003:DG2022_B A 1003 ? B 2022 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.365 -0.177 -0.043 10.292 -8.114 -2.845 4 A_DG1004:DC2021_B A 1004 ? B 2021 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.189 -0.195 -0.443 3.942 -20.661 4.985 5 A_DA1005:DT2020_B A 1005 ? B 2020 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.183 -0.189 -0.027 0.562 -13.458 6.953 6 A_DA1006:DT2019_B A 1006 ? B 2019 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.136 -0.182 0.007 0.724 -14.353 10.298 7 A_DT1007:DA2018_B A 1007 ? B 2018 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.109 -0.233 -0.304 -2.084 -18.398 5.279 8 A_DT1008:DA2017_B A 1008 ? B 2017 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.053 -0.177 -0.059 -8.031 -8.661 0.197 9 A_DC1009:DG2016_B A 1009 ? B 2016 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.068 -0.242 0.266 7.225 -8.021 -1.245 10 A_DG1010:DC2015_B A 1010 ? B 2015 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.195 -0.174 0.371 7.457 -25.121 -3.478 11 A_DC1011:DG2014_B A 1011 ? B 2014 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.428 -0.226 -0.316 9.995 25.409 -2.811 12 A_DG1012:DC2013_B A 1012 ? B 2013 ? 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 DG 2 1_555 B DC 11 1_555 -0.380 0.116 3.488 -0.017 6.516 32.538 -0.969 0.662 3.446 11.486 0.030 33.167 1 AA_DC1001DG1002:DC2023DG2024_BB A 1001 ? B 2024 ? A 1002 ? B 2023 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.900 0.596 3.274 0.095 -1.771 42.658 0.996 -1.227 3.250 -2.433 -0.130 42.693 2 AA_DG1002DC1003:DG2022DC2023_BB A 1002 ? B 2023 ? A 1003 ? B 2022 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.422 0.603 3.220 4.463 8.925 25.127 -0.996 2.048 3.127 19.558 -9.780 27.007 3 AA_DC1003DG1004:DC2021DG2022_BB A 1003 ? B 2022 ? A 1004 ? B 2021 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 0.044 0.173 3.459 3.321 5.221 40.012 -0.371 0.331 3.447 7.575 -4.819 40.468 4 AA_DG1004DA1005:DT2020DC2021_BB A 1004 ? B 2021 ? A 1005 ? B 2020 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.277 -0.230 3.219 -3.640 5.691 35.628 -1.149 -0.944 3.104 9.199 5.884 36.242 5 AA_DA1005DA1006:DT2019DT2020_BB A 1005 ? B 2020 ? A 1006 ? B 2019 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.083 -0.467 3.197 -0.323 -0.810 28.279 -0.771 -0.242 3.208 -1.658 0.661 28.292 6 AA_DA1006DT1007:DA2018DT2019_BB A 1006 ? B 2019 ? A 1007 ? B 2018 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.428 -0.028 3.217 3.088 1.033 37.479 -0.174 1.057 3.172 1.603 -4.795 37.615 7 AA_DT1007DT1008:DA2017DA2018_BB A 1007 ? B 2018 ? A 1008 ? B 2017 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 -0.022 0.221 3.413 0.409 -0.818 41.797 0.399 0.075 3.408 -1.146 -0.573 41.807 8 AA_DT1008DC1009:DG2016DA2017_BB A 1008 ? B 2017 ? A 1009 ? B 2016 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.369 1.063 3.211 -3.003 9.095 26.606 -0.002 -1.476 3.325 18.998 6.272 28.248 9 AA_DC1009DG1010:DC2015DG2016_BB A 1009 ? B 2016 ? A 1010 ? B 2015 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.028 0.790 3.310 -5.556 -13.595 44.819 2.108 0.830 3.060 -17.290 7.066 47.046 10 AA_DG1010DC1011:DG2014DC2015_BB A 1010 ? B 2015 ? A 1011 ? B 2014 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 1.450 0.583 3.574 5.717 -12.408 32.438 3.010 -1.460 3.338 -21.083 -9.715 35.126 11 AA_DC1011DG1012:DC2013DG2014_BB A 1011 ? B 2014 ? A 1012 ? B 2013 ? # _pdbx_initial_refinement_model.accession_code 2DBE _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details 'DNA PART OF NDB ENTRY GDL009' # _atom_sites.entry_id 1M6F _atom_sites.fract_transf_matrix[1][1] 0.041497 _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] 0.025112 _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] 0.015239 _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 MG N O P # loop_