data_358D # _entry.id 358D # _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 358D pdb_0000358d 10.2210/pdb358d/pdb RCSB GDJB55 ? ? WWPDB D_1000178827 ? ? # 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 2000-05-07 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-21 5 'Structure model' 1 4 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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 '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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_site 6 5 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 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 358D _pdbx_database_status.recvd_initial_deposition_date 1997-10-20 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mitra, S.N.' 1 'Chen, X.' 2 'Sundaralingam, M.' 3 # _citation.id primary _citation.title 'A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 26 _citation.page_first 5464 _citation.page_last 5471 _citation.year 1998 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9826773 _citation.pdbx_database_id_DOI 10.1093/nar/26.23.5464 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chen, X.' 1 ? primary 'Mitra, S.N.' 2 ? primary 'Rao, S.T.' 3 ? primary 'Sekar, K.' 4 ? primary 'Sundaralingam, M.' 5 ? # 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*(CBR)P*CP*CP*CP*IP*IP*IP*IP*I)-3') ; 3050.807 2 ? ? ? ? 2 non-polymer syn NETROPSIN 430.464 2 ? ? ? ? 3 water nat water 18.015 38 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(CBR)(DC)(DC)(DC)(DI)(DI)(DI)(DI)(DI)' _entity_poly.pdbx_seq_one_letter_code_can CCCCCIIIII _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 NETROPSIN NT 3 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 CBR n 1 3 DC n 1 4 DC n 1 5 DC n 1 6 DI n 1 7 DI n 1 8 DI n 1 9 DI n 1 10 DI 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 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DI 'DNA linking' y "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" ? 'C10 H13 N4 O7 P' 332.207 HOH non-polymer . WATER ? 'H2 O' 18.015 NT non-polymer . NETROPSIN ? 'C18 H26 N10 O3' 430.464 # 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 C A . n A 1 2 CBR 2 2 2 CBR C A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DI 6 6 6 DI I A . n A 1 7 DI 7 7 7 DI I A . n A 1 8 DI 8 8 8 DI I A . n A 1 9 DI 9 9 9 DI I A . n A 1 10 DI 10 10 10 DI I A . n B 1 1 DC 1 11 11 DC C B . n B 1 2 CBR 2 12 12 CBR C B . n B 1 3 DC 3 13 13 DC C B . n B 1 4 DC 4 14 14 DC C B . n B 1 5 DC 5 15 15 DC C B . n B 1 6 DI 6 16 16 DI I B . n B 1 7 DI 7 17 17 DI I B . n B 1 8 DI 8 18 18 DI I B . n B 1 9 DI 9 19 19 DI I B . n B 1 10 DI 10 20 20 DI I 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 NT 1 21 21 NT NT A . D 2 NT 1 22 22 NT NT A . E 3 HOH 1 23 23 HOH HOH A . E 3 HOH 2 24 24 HOH HOH A . E 3 HOH 3 25 25 HOH HOH A . E 3 HOH 4 26 26 HOH HOH A . E 3 HOH 5 30 30 HOH HOH A . E 3 HOH 6 32 32 HOH HOH A . E 3 HOH 7 33 33 HOH HOH A . E 3 HOH 8 34 34 HOH HOH A . E 3 HOH 9 37 37 HOH HOH A . E 3 HOH 10 38 38 HOH HOH A . E 3 HOH 11 39 39 HOH HOH A . E 3 HOH 12 40 40 HOH HOH A . E 3 HOH 13 41 41 HOH HOH A . E 3 HOH 14 43 43 HOH HOH A . E 3 HOH 15 45 45 HOH HOH A . E 3 HOH 16 49 49 HOH HOH A . E 3 HOH 17 51 51 HOH HOH A . E 3 HOH 18 52 52 HOH HOH A . E 3 HOH 19 53 53 HOH HOH A . E 3 HOH 20 54 54 HOH HOH A . E 3 HOH 21 55 55 HOH HOH A . E 3 HOH 22 56 56 HOH HOH A . E 3 HOH 23 57 57 HOH HOH A . E 3 HOH 24 60 60 HOH HOH A . F 3 HOH 1 27 27 HOH HOH B . F 3 HOH 2 28 28 HOH HOH B . F 3 HOH 3 29 29 HOH HOH B . F 3 HOH 4 31 31 HOH HOH B . F 3 HOH 5 35 35 HOH HOH B . F 3 HOH 6 36 36 HOH HOH B . F 3 HOH 7 42 42 HOH HOH B . F 3 HOH 8 44 44 HOH HOH B . F 3 HOH 9 46 46 HOH HOH B . F 3 HOH 10 47 47 HOH HOH B . F 3 HOH 11 48 48 HOH HOH B . F 3 HOH 12 50 50 HOH HOH B . F 3 HOH 13 58 58 HOH HOH B . F 3 HOH 14 59 59 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal AMoRE phasing . ? 1 X-PLOR refinement . ? 2 MSC 'data reduction' . ? 3 # _cell.entry_id 358D _cell.length_a 32.130 _cell.length_b 32.130 _cell.length_c 143.920 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 358D _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 # _exptl.entry_id 358D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 64.07 _exptl_crystal.density_Matthews 3.42 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, VAPOR DIFFUSION' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 293.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source ? _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 358D _reflns.observed_criterion_sigma_I 4.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 26.000 _reflns.d_resolution_high 2.500 _reflns.number_obs 1746 _reflns.number_all ? _reflns.percent_possible_obs 60.300 _reflns.pdbx_Rmerge_I_obs 0.059 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 3.140 _reflns.B_iso_Wilson_estimate 22.80 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.500 _reflns_shell.d_res_low 2.670 _reflns_shell.percent_possible_all 13.60 _reflns_shell.Rmerge_I_obs 0.139 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.100 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 358D _refine.ls_number_reflns_obs 1667 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 2.500 _refine.ls_percent_reflns_obs 60.300 _refine.ls_R_factor_obs 0.211 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.211 _refine.ls_R_factor_R_free 0.298 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.00 _refine.ls_number_reflns_R_free 163 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 17.80 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'D(CCCCCIIIII)' _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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 394 _refine_hist.pdbx_number_atoms_ligand 64 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 496 _refine_hist.d_res_high 2.500 _refine_hist.d_res_low 8.000 # 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 x_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d 1.690 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 21.2 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 1.38 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PARAM_ND.DNA TOP_NDBX.DNA 'X-RAY DIFFRACTION' 2 PARAM.NET TOPOLOGY.NET 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 358D _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 358D _struct.title 'CRYSTAL STRUCTURE OF THE 2:1 NETROPSIN-DNA DECAMER D(CBRCCCCIIIII) COMPLEX WITH END-TO-END BINDING' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 358D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, 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 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 358D _struct_ref.pdbx_db_accession 358D _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 358D A 1 ? 10 ? 358D 1 ? 10 ? 1 10 2 1 358D B 1 ? 10 ? 358D 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,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 covale1 covale both ? A DC 1 "O3'" ? ? ? 1_555 A CBR 2 P ? ? A DC 1 A CBR 2 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale2 covale both ? A CBR 2 "O3'" ? ? ? 1_555 A DC 3 P ? ? A CBR 2 A DC 3 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale3 covale both ? B DC 1 "O3'" ? ? ? 1_555 B CBR 2 P ? ? B DC 11 B CBR 12 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale4 covale both ? B CBR 2 "O3'" ? ? ? 1_555 B DC 3 P ? ? B CBR 12 B DC 13 1_555 ? ? ? ? ? ? ? 1.609 ? ? # _struct_conn_type.id covale _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 NT 21 ? 13 'BINDING SITE FOR RESIDUE NT A 21' AC2 Software A NT 22 ? 12 'BINDING SITE FOR RESIDUE NT A 22' 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 13 DC A 1 ? DC A 1 . ? 1_555 ? 2 AC1 13 CBR A 2 ? CBR A 2 . ? 1_555 ? 3 AC1 13 DC A 3 ? DC A 3 . ? 1_555 ? 4 AC1 13 DC A 4 ? DC A 4 . ? 1_555 ? 5 AC1 13 DC A 5 ? DC A 5 . ? 1_555 ? 6 AC1 13 DI A 6 ? DI A 6 . ? 1_555 ? 7 AC1 13 HOH E . ? HOH A 54 . ? 1_555 ? 8 AC1 13 HOH E . ? HOH A 55 . ? 1_555 ? 9 AC1 13 DC B 1 ? DC B 11 . ? 1_545 ? 10 AC1 13 CBR B 2 ? CBR B 12 . ? 1_545 ? 11 AC1 13 DI B 8 ? DI B 18 . ? 1_555 ? 12 AC1 13 DI B 9 ? DI B 19 . ? 1_555 ? 13 AC1 13 DI B 10 ? DI B 20 . ? 1_555 ? 14 AC2 12 DC A 1 ? DC A 1 . ? 1_565 ? 15 AC2 12 DI A 6 ? DI A 6 . ? 1_555 ? 16 AC2 12 DI A 7 ? DI A 7 . ? 1_555 ? 17 AC2 12 DI A 8 ? DI A 8 . ? 1_555 ? 18 AC2 12 DI A 9 ? DI A 9 . ? 1_555 ? 19 AC2 12 DI A 10 ? DI A 10 . ? 1_555 ? 20 AC2 12 HOH E . ? HOH A 55 . ? 1_565 ? 21 AC2 12 CBR B 2 ? CBR B 12 . ? 1_555 ? 22 AC2 12 DC B 3 ? DC B 13 . ? 1_555 ? 23 AC2 12 DC B 5 ? DC B 15 . ? 1_555 ? 24 AC2 12 DI B 6 ? DI B 16 . ? 1_555 ? 25 AC2 12 DI B 7 ? DI B 17 . ? 1_555 ? # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DI _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 6 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.053 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A CBR 2 A CBR 2 ? DC ? 2 B CBR 2 B CBR 12 ? DC ? # _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 CBR BR BR N N 1 CBR P P N N 2 CBR OP1 O N N 3 CBR OP2 O N N 4 CBR "O5'" O N N 5 CBR N1 N N N 6 CBR C6 C N N 7 CBR C2 C N N 8 CBR O2 O N N 9 CBR N3 N N N 10 CBR C4 C N N 11 CBR N4 N N N 12 CBR C5 C N N 13 CBR "C2'" C N N 14 CBR "C5'" C N N 15 CBR "C4'" C N R 16 CBR "O4'" O N N 17 CBR "C1'" C N R 18 CBR "C3'" C N S 19 CBR "O3'" O N N 20 CBR OP3 O N N 21 CBR HOP2 H N N 22 CBR H6 H N N 23 CBR H41 H N N 24 CBR H42 H N N 25 CBR "H2'" H N N 26 CBR "H2''" H N N 27 CBR "H5'" H N N 28 CBR "H5''" H N N 29 CBR "H4'" H N N 30 CBR "H1'" H N N 31 CBR "H3'" H N N 32 CBR "HO3'" H N N 33 CBR HOP3 H N N 34 DC OP3 O N N 35 DC P P N N 36 DC OP1 O N N 37 DC OP2 O N N 38 DC "O5'" O N N 39 DC "C5'" C N N 40 DC "C4'" C N R 41 DC "O4'" O N N 42 DC "C3'" C N S 43 DC "O3'" O N N 44 DC "C2'" C N N 45 DC "C1'" C N R 46 DC N1 N N N 47 DC C2 C N N 48 DC O2 O N N 49 DC N3 N N N 50 DC C4 C N N 51 DC N4 N N N 52 DC C5 C N N 53 DC C6 C N N 54 DC HOP3 H N N 55 DC HOP2 H N N 56 DC "H5'" H N N 57 DC "H5''" H N N 58 DC "H4'" H N N 59 DC "H3'" H N N 60 DC "HO3'" H N N 61 DC "H2'" H N N 62 DC "H2''" H N N 63 DC "H1'" H N N 64 DC H41 H N N 65 DC H42 H N N 66 DC H5 H N N 67 DC H6 H N N 68 DI OP3 O N N 69 DI P P N N 70 DI OP1 O N N 71 DI OP2 O N N 72 DI "O5'" O N N 73 DI "C5'" C N N 74 DI "C4'" C N R 75 DI "O4'" O N N 76 DI "C3'" C N S 77 DI "O3'" O N N 78 DI "C2'" C N N 79 DI "C1'" C N R 80 DI N9 N Y N 81 DI C8 C Y N 82 DI N7 N Y N 83 DI C5 C Y N 84 DI C6 C N N 85 DI O6 O N N 86 DI N1 N N N 87 DI C2 C N N 88 DI N3 N N N 89 DI C4 C Y N 90 DI HOP3 H N N 91 DI HOP2 H N N 92 DI "H5'" H N N 93 DI "H5''" H N N 94 DI "H4'" H N N 95 DI "H3'" H N N 96 DI "HO3'" H N N 97 DI "H2'" H N N 98 DI "H2''" H N N 99 DI "H1'" H N N 100 DI H8 H N N 101 DI H1 H N N 102 DI H2 H N N 103 HOH O O N N 104 HOH H1 H N N 105 HOH H2 H N N 106 NT C1 C N N 107 NT N1 N N N 108 NT N2 N N N 109 NT N3 N N N 110 NT C2 C N N 111 NT C3 C N N 112 NT O1 O N N 113 NT N4 N N N 114 NT C4 C Y N 115 NT C5 C Y N 116 NT C6 C Y N 117 NT N5 N Y N 118 NT C8 C N N 119 NT C7 C Y N 120 NT C9 C N N 121 NT O2 O N N 122 NT N6 N N N 123 NT C10 C Y N 124 NT C11 C Y N 125 NT C12 C Y N 126 NT N7 N Y N 127 NT C14 C N N 128 NT C13 C Y N 129 NT C15 C N N 130 NT O3 O N N 131 NT N8 N N N 132 NT C16 C N N 133 NT C17 C N N 134 NT C18 C N N 135 NT N9 N N N 136 NT N10 N N N 137 NT HN1 H N N 138 NT HN21 H N N 139 NT HN22 H N N 140 NT HN3 H N N 141 NT H21 H N N 142 NT H22 H N N 143 NT HN4 H N N 144 NT H5 H N N 145 NT H81 H N N 146 NT H82 H N N 147 NT H83 H N N 148 NT H7 H N N 149 NT HN6 H N N 150 NT H11 H N N 151 NT H141 H N N 152 NT H142 H N N 153 NT H143 H N N 154 NT H13 H N N 155 NT HN8 H N N 156 NT H161 H N N 157 NT H162 H N N 158 NT H171 H N N 159 NT H172 H N N 160 NT HN9 H N N 161 NT HN01 H N N 162 NT HN02 H N N 163 # 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 CBR BR C5 sing N N 1 CBR P OP1 doub N N 2 CBR P OP2 sing N N 3 CBR P "O5'" sing N N 4 CBR P OP3 sing N N 5 CBR OP2 HOP2 sing N N 6 CBR "O5'" "C5'" sing N N 7 CBR N1 C6 sing N N 8 CBR N1 C2 sing N N 9 CBR N1 "C1'" sing N N 10 CBR C6 C5 doub N N 11 CBR C6 H6 sing N N 12 CBR C2 O2 doub N N 13 CBR C2 N3 sing N N 14 CBR N3 C4 doub N N 15 CBR C4 N4 sing N N 16 CBR C4 C5 sing N N 17 CBR N4 H41 sing N N 18 CBR N4 H42 sing N N 19 CBR "C2'" "C1'" sing N N 20 CBR "C2'" "C3'" sing N N 21 CBR "C2'" "H2'" sing N N 22 CBR "C2'" "H2''" sing N N 23 CBR "C5'" "C4'" sing N N 24 CBR "C5'" "H5'" sing N N 25 CBR "C5'" "H5''" sing N N 26 CBR "C4'" "O4'" sing N N 27 CBR "C4'" "C3'" sing N N 28 CBR "C4'" "H4'" sing N N 29 CBR "O4'" "C1'" sing N N 30 CBR "C1'" "H1'" sing N N 31 CBR "C3'" "O3'" sing N N 32 CBR "C3'" "H3'" sing N N 33 CBR "O3'" "HO3'" sing N N 34 CBR OP3 HOP3 sing N N 35 DC OP3 P sing N N 36 DC OP3 HOP3 sing N N 37 DC P OP1 doub N N 38 DC P OP2 sing N N 39 DC P "O5'" sing N N 40 DC OP2 HOP2 sing N N 41 DC "O5'" "C5'" sing N N 42 DC "C5'" "C4'" sing N N 43 DC "C5'" "H5'" sing N N 44 DC "C5'" "H5''" sing N N 45 DC "C4'" "O4'" sing N N 46 DC "C4'" "C3'" sing N N 47 DC "C4'" "H4'" sing N N 48 DC "O4'" "C1'" sing N N 49 DC "C3'" "O3'" sing N N 50 DC "C3'" "C2'" sing N N 51 DC "C3'" "H3'" sing N N 52 DC "O3'" "HO3'" sing N N 53 DC "C2'" "C1'" sing N N 54 DC "C2'" "H2'" sing N N 55 DC "C2'" "H2''" sing N N 56 DC "C1'" N1 sing N N 57 DC "C1'" "H1'" sing N N 58 DC N1 C2 sing N N 59 DC N1 C6 sing N N 60 DC C2 O2 doub N N 61 DC C2 N3 sing N N 62 DC N3 C4 doub N N 63 DC C4 N4 sing N N 64 DC C4 C5 sing N N 65 DC N4 H41 sing N N 66 DC N4 H42 sing N N 67 DC C5 C6 doub N N 68 DC C5 H5 sing N N 69 DC C6 H6 sing N N 70 DI OP3 P sing N N 71 DI OP3 HOP3 sing N N 72 DI P OP1 doub N N 73 DI P OP2 sing N N 74 DI P "O5'" sing N N 75 DI OP2 HOP2 sing N N 76 DI "O5'" "C5'" sing N N 77 DI "C5'" "C4'" sing N N 78 DI "C5'" "H5'" sing N N 79 DI "C5'" "H5''" sing N N 80 DI "C4'" "O4'" sing N N 81 DI "C4'" "C3'" sing N N 82 DI "C4'" "H4'" sing N N 83 DI "O4'" "C1'" sing N N 84 DI "C3'" "O3'" sing N N 85 DI "C3'" "C2'" sing N N 86 DI "C3'" "H3'" sing N N 87 DI "O3'" "HO3'" sing N N 88 DI "C2'" "C1'" sing N N 89 DI "C2'" "H2'" sing N N 90 DI "C2'" "H2''" sing N N 91 DI "C1'" N9 sing N N 92 DI "C1'" "H1'" sing N N 93 DI N9 C8 sing Y N 94 DI N9 C4 sing Y N 95 DI C8 N7 doub Y N 96 DI C8 H8 sing N N 97 DI N7 C5 sing Y N 98 DI C5 C6 sing N N 99 DI C5 C4 doub Y N 100 DI C6 O6 doub N N 101 DI C6 N1 sing N N 102 DI N1 C2 sing N N 103 DI N1 H1 sing N N 104 DI C2 N3 doub N N 105 DI C2 H2 sing N N 106 DI N3 C4 sing N N 107 HOH O H1 sing N N 108 HOH O H2 sing N N 109 NT C1 N1 doub N N 110 NT C1 N2 sing N N 111 NT C1 N3 sing N N 112 NT N1 HN1 sing N N 113 NT N2 HN21 sing N N 114 NT N2 HN22 sing N N 115 NT N3 C2 sing N N 116 NT N3 HN3 sing N N 117 NT C2 C3 sing N N 118 NT C2 H21 sing N N 119 NT C2 H22 sing N N 120 NT C3 O1 doub N N 121 NT C3 N4 sing N N 122 NT N4 C4 sing N N 123 NT N4 HN4 sing N N 124 NT C4 C5 sing Y N 125 NT C4 C7 doub Y N 126 NT C5 C6 doub Y N 127 NT C5 H5 sing N N 128 NT C6 N5 sing Y N 129 NT C6 C9 sing N N 130 NT N5 C8 sing N N 131 NT N5 C7 sing Y N 132 NT C8 H81 sing N N 133 NT C8 H82 sing N N 134 NT C8 H83 sing N N 135 NT C7 H7 sing N N 136 NT C9 O2 doub N N 137 NT C9 N6 sing N N 138 NT N6 C10 sing N N 139 NT N6 HN6 sing N N 140 NT C10 C11 sing Y N 141 NT C10 C13 doub Y N 142 NT C11 C12 doub Y N 143 NT C11 H11 sing N N 144 NT C12 N7 sing Y N 145 NT C12 C15 sing N N 146 NT N7 C14 sing N N 147 NT N7 C13 sing Y N 148 NT C14 H141 sing N N 149 NT C14 H142 sing N N 150 NT C14 H143 sing N N 151 NT C13 H13 sing N N 152 NT C15 O3 doub N N 153 NT C15 N8 sing N N 154 NT N8 C16 sing N N 155 NT N8 HN8 sing N N 156 NT C16 C17 sing N N 157 NT C16 H161 sing N N 158 NT C16 H162 sing N N 159 NT C17 C18 sing N N 160 NT C17 H171 sing N N 161 NT C17 H172 sing N N 162 NT C18 N9 doub N N 163 NT C18 N10 sing N N 164 NT N9 HN9 sing N N 165 NT N10 HN01 sing N N 166 NT N10 HN02 sing N N 167 # _pdbx_initial_refinement_model.accession_code ? _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 Other _pdbx_initial_refinement_model.details 'fiber B-DNA' # _atom_sites.entry_id 358D _atom_sites.fract_transf_matrix[1][1] 0.031124 _atom_sites.fract_transf_matrix[1][2] 0.017969 _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] 0.035938 _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] 0.006948 _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 BR C N O P # loop_