data_1Z8V # _entry.id 1Z8V # _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 1Z8V pdb_00001z8v 10.2210/pdb1z8v/pdb NDB BD0078 ? ? RCSB RCSB032444 ? ? WWPDB D_1000032444 ? ? # 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 2006-03-14 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 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' diffrn_source 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' '_diffrn_source.pdbx_synchrotron_site' 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 1Z8V _pdbx_database_status.recvd_initial_deposition_date 2005-03-31 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 'Van Hecke, K.' 1 'Nam, P.C.' 2 'Nguyen, M.T.' 3 'Van Meervelt, L.' 4 # _citation.id primary _citation.title ;Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations. ; _citation.journal_abbrev 'Febs J.' _citation.journal_volume 272 _citation.page_first 3531 _citation.page_last 3541 _citation.year 2005 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1742-464X _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16008554 _citation.pdbx_database_id_DOI 10.1111/j.1742-4658.2005.04773.x # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Van Hecke, K.' 1 ? primary 'Nam, P.C.' 2 ? primary 'Nguyen, M.T.' 3 ? primary 'Van Meervelt, L.' 4 ? # 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(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')" 3085.029 2 ? ? ? ? 2 non-polymer syn NETROPSIN 430.464 1 ? ? ? ? 3 water nat water 18.015 68 ? ? ? ? # _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 '(DG)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can GGCCAATTGG _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 DG n 1 2 DG n 1 3 DC n 1 4 DC n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DG n 1 10 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _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 'The oligonucleotide was purchased from Oswel DNA service (University of Southampton, UK)' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 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 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 DG 1 1 1 DG G A . n A 1 2 DG 2 2 2 DG G 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 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DG 1 21 21 DG G B . n B 1 2 DG 2 22 22 DG G B . n B 1 3 DC 3 23 23 DC C B . n B 1 4 DC 4 24 24 DC C B . n B 1 5 DA 5 25 25 DA A B . n B 1 6 DA 6 26 26 DA A B . n B 1 7 DT 7 27 27 DT T B . n B 1 8 DT 8 28 28 DT T B . n B 1 9 DG 9 29 29 DG G B . n B 1 10 DG 10 30 30 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 NT 1 31 31 NT NT B . D 3 HOH 1 102 102 HOH HOH A . D 3 HOH 2 104 104 HOH HOH A . D 3 HOH 3 105 105 HOH HOH A . D 3 HOH 4 106 106 HOH HOH A . D 3 HOH 5 108 108 HOH HOH A . D 3 HOH 6 112 112 HOH HOH A . D 3 HOH 7 113 113 HOH HOH A . D 3 HOH 8 115 115 HOH HOH A . D 3 HOH 9 116 116 HOH HOH A . D 3 HOH 10 118 118 HOH HOH A . D 3 HOH 11 120 120 HOH HOH A . D 3 HOH 12 123 123 HOH HOH A . D 3 HOH 13 124 124 HOH HOH A . D 3 HOH 14 125 125 HOH HOH A . D 3 HOH 15 127 127 HOH HOH A . D 3 HOH 16 130 130 HOH HOH A . D 3 HOH 17 131 131 HOH HOH A . D 3 HOH 18 133 133 HOH HOH A . D 3 HOH 19 137 137 HOH HOH A . D 3 HOH 20 144 144 HOH HOH A . D 3 HOH 21 145 145 HOH HOH A . D 3 HOH 22 147 147 HOH HOH A . D 3 HOH 23 151 151 HOH HOH A . D 3 HOH 24 152 152 HOH HOH A . D 3 HOH 25 154 154 HOH HOH A . D 3 HOH 26 159 159 HOH HOH A . D 3 HOH 27 161 161 HOH HOH A . D 3 HOH 28 162 162 HOH HOH A . D 3 HOH 29 163 163 HOH HOH A . D 3 HOH 30 165 165 HOH HOH A . D 3 HOH 31 167 167 HOH HOH A . D 3 HOH 32 168 168 HOH HOH A . E 3 HOH 1 101 101 HOH HOH B . E 3 HOH 2 103 103 HOH HOH B . E 3 HOH 3 107 107 HOH HOH B . E 3 HOH 4 109 109 HOH HOH B . E 3 HOH 5 110 110 HOH HOH B . E 3 HOH 6 111 111 HOH HOH B . E 3 HOH 7 114 114 HOH HOH B . E 3 HOH 8 117 117 HOH HOH B . E 3 HOH 9 119 119 HOH HOH B . E 3 HOH 10 121 121 HOH HOH B . E 3 HOH 11 122 122 HOH HOH B . E 3 HOH 12 126 126 HOH HOH B . E 3 HOH 13 128 128 HOH HOH B . E 3 HOH 14 129 129 HOH HOH B . E 3 HOH 15 132 132 HOH HOH B . E 3 HOH 16 134 134 HOH HOH B . E 3 HOH 17 135 135 HOH HOH B . E 3 HOH 18 136 136 HOH HOH B . E 3 HOH 19 138 138 HOH HOH B . E 3 HOH 20 139 139 HOH HOH B . E 3 HOH 21 140 140 HOH HOH B . E 3 HOH 22 141 141 HOH HOH B . E 3 HOH 23 142 142 HOH HOH B . E 3 HOH 24 143 143 HOH HOH B . E 3 HOH 25 146 146 HOH HOH B . E 3 HOH 26 148 148 HOH HOH B . E 3 HOH 27 149 149 HOH HOH B . E 3 HOH 28 150 150 HOH HOH B . E 3 HOH 29 153 153 HOH HOH B . E 3 HOH 30 155 155 HOH HOH B . E 3 HOH 31 156 156 HOH HOH B . E 3 HOH 32 157 157 HOH HOH B . E 3 HOH 33 158 158 HOH HOH B . E 3 HOH 34 160 160 HOH HOH B . E 3 HOH 35 164 164 HOH HOH B . E 3 HOH 36 166 166 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 REFMAC refinement 5.1.24 ? 3 # _cell.entry_id 1Z8V _cell.length_a 26.025 _cell.length_b 38.559 _cell.length_c 53.203 _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 1Z8V _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 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1Z8V _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.16 _exptl_crystal.density_percent_sol 43.14 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'potassium cacodylate, MPD, magnesium chloride, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K' _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.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'potassium cacodylate' ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'magnesium chloride' ? ? ? 1 4 1 spermine ? ? ? 1 5 2 MPD ? ? ? 1 6 2 'magnesium chloride' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2003-01-21 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8457 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7B' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW7B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.8457 # _reflns.entry_id 1Z8V _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 1.75 _reflns.d_resolution_low 20 _reflns.number_all ? _reflns.number_obs 5724 _reflns.percent_possible_obs 98.1 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.04 _reflns.pdbx_netI_over_sigmaI 20.1 _reflns.B_iso_Wilson_estimate 24.74 _reflns.pdbx_redundancy 10.7 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.75 _reflns_shell.d_res_low 1.81 _reflns_shell.percent_possible_all 96.2 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.199 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 538 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1Z8V _refine.ls_d_res_high 1.75 _refine.ls_d_res_low 9.6 _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 5379 _refine.ls_number_reflns_R_free ? _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_all 0.2 _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1997 _refine.ls_R_factor_R_free ? _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 'NDB ENTRY DD0002' _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _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 isotropic _refine.B_iso_mean 35.7 _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_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _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 410 _refine_hist.pdbx_number_atoms_ligand 31 _refine_hist.number_atoms_solvent 68 _refine_hist.number_atoms_total 509 _refine_hist.d_res_high 1.75 _refine_hist.d_res_low 9.6 # _database_PDB_matrix.entry_id 1Z8V _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 1Z8V _struct.title 'The Structure of d(GGCCAATTGG) Complexed with Netropsin' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Z8V _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA DOUBLE HELIX, BASE TRIPLETS, MINOR GROOVE BINDER, DRUG, NETROPSIN, 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 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1Z8V _struct_ref.pdbx_db_accession 1Z8V _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 1Z8V A 1 ? 10 ? 1Z8V 1 ? 10 ? 1 10 2 1 1Z8V B 1 ? 10 ? 1Z8V 21 ? 30 ? 21 30 # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 4 B DG 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 4 B DG 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 4 B DG 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 9 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 9 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 9 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B NT 31 ? 15 'BINDING SITE FOR RESIDUE NT B 31' 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 15 DA A 5 ? DA A 5 . ? 1_555 ? 2 AC1 15 DA A 6 ? DA A 6 . ? 1_555 ? 3 AC1 15 DT A 7 ? DT A 7 . ? 1_555 ? 4 AC1 15 DT A 8 ? DT A 8 . ? 1_555 ? 5 AC1 15 DG A 9 ? DG A 9 . ? 1_555 ? 6 AC1 15 DA B 5 ? DA B 25 . ? 1_555 ? 7 AC1 15 DA B 6 ? DA B 26 . ? 1_555 ? 8 AC1 15 DT B 7 ? DT B 27 . ? 1_555 ? 9 AC1 15 DT B 8 ? DT B 28 . ? 1_555 ? 10 AC1 15 DG B 9 ? DG B 29 . ? 1_555 ? 11 AC1 15 DG B 10 ? DG B 30 . ? 1_555 ? 12 AC1 15 HOH E . ? HOH B 117 . ? 1_555 ? 13 AC1 15 HOH E . ? HOH B 140 . ? 1_555 ? 14 AC1 15 HOH E . ? HOH B 157 . ? 1_555 ? 15 AC1 15 HOH E . ? HOH B 160 . ? 1_555 ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 112 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 167 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 3_655 _pdbx_validate_symm_contact.dist 2.15 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DG 2 ? ? "C3'" A DG 2 ? ? 1.355 1.419 -0.064 0.006 N 2 1 C5 A DG 2 ? ? N7 A DG 2 ? ? 1.429 1.388 0.041 0.006 N 3 1 "O3'" A DT 8 ? ? "C3'" A DT 8 ? ? 1.381 1.419 -0.038 0.006 N 4 1 C5 A DG 10 ? ? N7 A DG 10 ? ? 1.427 1.388 0.039 0.006 N 5 1 C6 B DA 26 ? ? N1 B DA 26 ? ? 1.297 1.351 -0.054 0.007 N 6 1 "O3'" B DT 27 ? ? "C3'" B DT 27 ? ? 1.381 1.419 -0.038 0.006 N 7 1 "O3'" B DT 28 ? ? "C3'" B DT 28 ? ? 1.356 1.419 -0.063 0.006 N # 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 DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 101.46 108.00 -6.54 0.70 N 2 1 C8 A DG 1 ? ? N9 A DG 1 ? ? C4 A DG 1 ? ? 103.22 106.40 -3.18 0.40 N 3 1 N9 A DG 1 ? ? C4 A DG 1 ? ? C5 A DG 1 ? ? 107.97 105.40 2.57 0.40 N 4 1 N3 A DG 1 ? ? C4 A DG 1 ? ? N9 A DG 1 ? ? 122.04 126.00 -3.96 0.60 N 5 1 N1 A DG 1 ? ? C2 A DG 1 ? ? N2 A DG 1 ? ? 123.07 116.20 6.87 0.90 N 6 1 N3 A DG 1 ? ? C2 A DG 1 ? ? N2 A DG 1 ? ? 113.99 119.90 -5.91 0.70 N 7 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 116.13 111.50 4.63 0.50 N 8 1 C5 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 124.80 128.60 -3.80 0.60 N 9 1 OP1 A DC 3 ? ? P A DC 3 ? ? OP2 A DC 3 ? ? 129.42 119.60 9.82 1.50 N 10 1 C2 A DC 3 ? ? N3 A DC 3 ? ? C4 A DC 3 ? ? 123.54 119.90 3.64 0.50 N 11 1 OP1 A DC 4 ? ? P A DC 4 ? ? OP2 A DC 4 ? ? 130.84 119.60 11.24 1.50 N 12 1 "O5'" A DC 4 ? ? "C5'" A DC 4 ? ? "C4'" A DC 4 ? ? 104.20 109.40 -5.20 0.80 N 13 1 "C3'" A DC 4 ? ? "C2'" A DC 4 ? ? "C1'" A DC 4 ? ? 93.12 102.40 -9.28 0.80 N 14 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 114.16 108.30 5.86 0.30 N 15 1 C6 A DC 4 ? ? N1 A DC 4 ? ? C2 A DC 4 ? ? 123.16 120.30 2.86 0.40 N 16 1 N3 A DC 4 ? ? C4 A DC 4 ? ? C5 A DC 4 ? ? 125.07 121.90 3.17 0.40 N 17 1 N1 A DA 5 ? ? C6 A DA 5 ? ? N6 A DA 5 ? ? 122.39 118.60 3.79 0.60 N 18 1 C5 A DA 6 ? ? N7 A DA 6 ? ? C8 A DA 6 ? ? 100.31 103.90 -3.59 0.50 N 19 1 OP1 A DT 7 ? ? P A DT 7 ? ? OP2 A DT 7 ? ? 129.96 119.60 10.36 1.50 N 20 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 102.41 108.00 -5.59 0.70 N 21 1 C6 A DT 7 ? ? N1 A DT 7 ? ? C2 A DT 7 ? ? 118.26 121.30 -3.04 0.50 N 22 1 N3 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 125.85 119.90 5.95 0.60 N 23 1 C5 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 119.62 124.90 -5.28 0.70 N 24 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 102.36 108.00 -5.64 0.70 N 25 1 C4 A DG 9 ? ? C5 A DG 9 ? ? N7 A DG 9 ? ? 113.34 110.80 2.54 0.40 N 26 1 C5 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 124.88 128.60 -3.72 0.60 N 27 1 "O4'" B DG 21 ? ? "C1'" B DG 21 ? ? N9 B DG 21 ? ? 103.14 108.00 -4.86 0.70 N 28 1 C4 B DG 21 ? ? C5 B DG 21 ? ? N7 B DG 21 ? ? 113.76 110.80 2.96 0.40 N 29 1 N1 B DG 21 ? ? C6 B DG 21 ? ? O6 B DG 21 ? ? 123.93 119.90 4.03 0.60 N 30 1 C5 B DG 21 ? ? C6 B DG 21 ? ? O6 B DG 21 ? ? 123.63 128.60 -4.97 0.60 N 31 1 "C3'" B DC 23 ? ? "O3'" B DC 23 ? ? P B DC 24 ? ? 111.88 119.70 -7.82 1.20 Y 32 1 "O5'" B DC 24 ? ? "C5'" B DC 24 ? ? "C4'" B DC 24 ? ? 103.20 109.40 -6.20 0.80 N 33 1 "O4'" B DC 24 ? ? "C4'" B DC 24 ? ? "C3'" B DC 24 ? ? 102.10 104.50 -2.40 0.40 N 34 1 "O4'" B DC 24 ? ? "C1'" B DC 24 ? ? N1 B DC 24 ? ? 102.58 108.00 -5.42 0.70 N 35 1 C2 B DC 24 ? ? N3 B DC 24 ? ? C4 B DC 24 ? ? 126.49 119.90 6.59 0.50 N 36 1 N3 B DC 24 ? ? C4 B DC 24 ? ? C5 B DC 24 ? ? 118.27 121.90 -3.63 0.40 N 37 1 N1 B DC 24 ? ? C2 B DC 24 ? ? O2 B DC 24 ? ? 123.86 118.90 4.96 0.60 N 38 1 "O4'" B DA 25 ? ? "C1'" B DA 25 ? ? N9 B DA 25 ? ? 112.36 108.30 4.06 0.30 N 39 1 "O4'" B DA 26 ? ? "C1'" B DA 26 ? ? N9 B DA 26 ? ? 103.39 108.00 -4.61 0.70 N 40 1 C5 B DA 26 ? ? C6 B DA 26 ? ? N1 B DA 26 ? ? 114.70 117.70 -3.00 0.50 N 41 1 "O5'" B DG 29 ? ? P B DG 29 ? ? OP1 B DG 29 ? ? 100.13 105.70 -5.57 0.90 N 42 1 "O4'" B DG 29 ? ? "C1'" B DG 29 ? ? N9 B DG 29 ? ? 103.16 108.00 -4.84 0.70 N 43 1 N3 B DG 29 ? ? C2 B DG 29 ? ? N2 B DG 29 ? ? 115.16 119.90 -4.74 0.70 N 44 1 N1 B DG 30 ? ? C6 B DG 30 ? ? O6 B DG 30 ? ? 123.92 119.90 4.02 0.60 N 45 1 C5 B DG 30 ? ? C6 B DG 30 ? ? O6 B DG 30 ? ? 123.05 128.60 -5.55 0.60 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 NT C1 C N N 147 NT N1 N N N 148 NT N2 N N N 149 NT N3 N N N 150 NT C2 C N N 151 NT C3 C N N 152 NT O1 O N N 153 NT N4 N N N 154 NT C4 C Y N 155 NT C5 C Y N 156 NT C6 C Y N 157 NT N5 N Y N 158 NT C8 C N N 159 NT C7 C Y N 160 NT C9 C N N 161 NT O2 O N N 162 NT N6 N N N 163 NT C10 C Y N 164 NT C11 C Y N 165 NT C12 C Y N 166 NT N7 N Y N 167 NT C14 C N N 168 NT C13 C Y N 169 NT C15 C N N 170 NT O3 O N N 171 NT N8 N N N 172 NT C16 C N N 173 NT C17 C N N 174 NT C18 C N N 175 NT N9 N N N 176 NT N10 N N N 177 NT HN1 H N N 178 NT HN21 H N N 179 NT HN22 H N N 180 NT HN3 H N N 181 NT H21 H N N 182 NT H22 H N N 183 NT HN4 H N N 184 NT H5 H N N 185 NT H81 H N N 186 NT H82 H N N 187 NT H83 H N N 188 NT H7 H N N 189 NT HN6 H N N 190 NT H11 H N N 191 NT H141 H N N 192 NT H142 H N N 193 NT H143 H N N 194 NT H13 H N N 195 NT HN8 H N N 196 NT H161 H N N 197 NT H162 H N N 198 NT H171 H N N 199 NT H172 H N N 200 NT HN9 H N N 201 NT HN01 H N N 202 NT HN02 H N N 203 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 NT C1 N1 doub N N 152 NT C1 N2 sing N N 153 NT C1 N3 sing N N 154 NT N1 HN1 sing N N 155 NT N2 HN21 sing N N 156 NT N2 HN22 sing N N 157 NT N3 C2 sing N N 158 NT N3 HN3 sing N N 159 NT C2 C3 sing N N 160 NT C2 H21 sing N N 161 NT C2 H22 sing N N 162 NT C3 O1 doub N N 163 NT C3 N4 sing N N 164 NT N4 C4 sing N N 165 NT N4 HN4 sing N N 166 NT C4 C5 sing Y N 167 NT C4 C7 doub Y N 168 NT C5 C6 doub Y N 169 NT C5 H5 sing N N 170 NT C6 N5 sing Y N 171 NT C6 C9 sing N N 172 NT N5 C8 sing N N 173 NT N5 C7 sing Y N 174 NT C8 H81 sing N N 175 NT C8 H82 sing N N 176 NT C8 H83 sing N N 177 NT C7 H7 sing N N 178 NT C9 O2 doub N N 179 NT C9 N6 sing N N 180 NT N6 C10 sing N N 181 NT N6 HN6 sing N N 182 NT C10 C11 sing Y N 183 NT C10 C13 doub Y N 184 NT C11 C12 doub Y N 185 NT C11 H11 sing N N 186 NT C12 N7 sing Y N 187 NT C12 C15 sing N N 188 NT N7 C14 sing N N 189 NT N7 C13 sing Y N 190 NT C14 H141 sing N N 191 NT C14 H142 sing N N 192 NT C14 H143 sing N N 193 NT C13 H13 sing N N 194 NT C15 O3 doub N N 195 NT C15 N8 sing N N 196 NT N8 C16 sing N N 197 NT N8 HN8 sing N N 198 NT C16 C17 sing N N 199 NT C16 H161 sing N N 200 NT C16 H162 sing N N 201 NT C17 C18 sing N N 202 NT C17 H171 sing N N 203 NT C17 H172 sing N N 204 NT C18 N9 doub N N 205 NT C18 N10 sing N N 206 NT N9 HN9 sing N N 207 NT N10 HN01 sing N N 208 NT N10 HN02 sing N N 209 # _ndb_struct_conf_na.entry_id 1Z8V _ndb_struct_conf_na.feature '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 3 1_555 B DG 10 1_555 0.358 -0.178 -0.149 10.451 -19.101 -1.679 1 A_DC3:DG30_B A 3 ? B 30 ? 19 1 1 A DC 4 1_555 B DG 9 1_555 0.265 -0.167 -0.291 16.799 -6.182 -1.939 2 A_DC4:DG29_B A 4 ? B 29 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.069 -0.096 -0.083 6.827 -16.531 6.807 3 A_DA5:DT28_B A 5 ? B 28 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.222 -0.074 0.056 2.970 -20.062 6.652 4 A_DA6:DT27_B A 6 ? B 27 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.167 -0.020 -0.135 -3.197 -19.438 8.200 5 A_DT7:DA26_B A 7 ? B 26 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.020 -0.160 -0.055 -5.959 -12.609 4.991 6 A_DT8:DA25_B A 8 ? B 25 ? 20 1 1 A DG 9 1_555 B DC 4 1_555 -0.343 -0.156 -0.005 -6.732 -8.377 -0.369 7 A_DG9:DC24_B A 9 ? B 24 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.008 -0.137 0.110 -1.622 -11.493 -3.639 8 A_DG10:DC23_B A 10 ? B 23 ? 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 3 1_555 B DG 10 1_555 A DC 4 1_555 B DG 9 1_555 0.676 0.056 3.261 5.854 10.332 25.276 -2.412 0.031 3.121 22.121 -12.533 27.886 1 AA_DC3DC4:DG29DG30_BB A 3 ? B 30 ? A 4 ? B 29 ? 1 A DC 4 1_555 B DG 9 1_555 A DA 5 1_555 B DT 8 1_555 0.261 0.799 3.509 1.182 6.410 46.461 0.426 -0.222 3.588 8.078 -1.490 46.891 2 AA_DC4DA5:DT28DG29_BB A 4 ? B 29 ? A 5 ? B 28 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.208 0.063 3.332 -2.925 5.678 33.761 -0.802 -0.116 3.304 9.670 4.980 34.342 3 AA_DA5DA6:DT27DT28_BB A 5 ? B 28 ? A 6 ? B 27 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.043 -0.639 3.326 1.572 -1.602 33.412 -0.840 0.338 3.346 -2.783 -2.730 33.485 4 AA_DA6DT7:DA26DT27_BB A 6 ? B 27 ? A 7 ? B 26 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 0.555 0.474 3.311 2.111 4.399 39.088 0.169 -0.567 3.366 6.543 -3.141 39.379 5 AA_DT7DT8:DA25DA26_BB A 7 ? B 26 ? A 8 ? B 25 ? 1 A DT 8 1_555 B DA 5 1_555 A DG 9 1_555 B DC 4 1_555 -0.519 0.008 3.348 -1.170 7.509 30.192 -1.462 0.738 3.272 14.137 2.203 31.112 6 AA_DT8DG9:DC24DA25_BB A 8 ? B 25 ? A 9 ? B 24 ? 1 A DG 9 1_555 B DC 4 1_555 A DG 10 1_555 B DC 3 1_555 0.161 -0.350 3.198 -1.773 8.731 33.286 -1.903 -0.538 3.001 14.913 3.028 34.425 7 AA_DG9DG10:DC23DC24_BB A 9 ? B 24 ? A 10 ? B 23 ? # _pdbx_initial_refinement_model.accession_code 432D _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 'NDB ENTRY DD0002' # _atom_sites.entry_id 1Z8V _atom_sites.fract_transf_matrix[1][1] 0.038425 _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] 0.025934 _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] 0.018796 _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 N O P # loop_