data_1PLY # _entry.id 1PLY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1PLY pdb_00001ply 10.2210/pdb1ply/pdb WWPDB D_1000175731 ? ? # 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 1995-06-03 2 'Structure model' 1 1 2008-03-03 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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 4 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_database_status 5 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_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 1PLY _pdbx_database_status.recvd_initial_deposition_date 1995-02-28 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Chandrasekaran, R.' 1 'Radha, A.' 2 'Park, H.-S.' 3 # _citation.id primary _citation.title 'Sodium ions and water molecules in the structure of poly(dA).poly(dT).' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 51 _citation.page_first 1025 _citation.page_last 1035 _citation.year 1995 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15299771 _citation.pdbx_database_id_DOI 10.1107/S0907444995001880 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chandrasekaran, R.' 1 ? primary 'Radha, A.' 2 ? primary 'Park, H.S.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(P*AP*AP*AP*AP*A)-3') ; 1521.077 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*TP*TP*TP*TP*T)-3') ; 1476.007 1 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 10 ? ? ? ? 4 water nat water 18.015 16 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DA)(DA)(DA)(DA)(DA)' AAAAA A ? 2 polydeoxyribonucleotide no no '(DT)(DT)(DT)(DT)(DT)' TTTTT B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'SODIUM ION' NA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DA n 1 3 DA n 1 4 DA n 1 5 DA n 2 1 DT n 2 2 DT n 2 3 DT n 2 4 DT n 2 5 DT 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DA 1 1 1 DA A A . n A 1 2 DA 2 2 2 DA A A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DA 5 5 5 DA A A . n B 2 1 DT 1 6 6 DT T B . n B 2 2 DT 2 7 7 DT T B . n B 2 3 DT 3 8 8 DT T B . n B 2 4 DT 4 9 9 DT T B . n B 2 5 DT 5 10 10 DT T 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 3 NA 1 6 3 NA NA A . D 3 NA 1 7 4 NA NA A . E 3 NA 1 8 5 NA NA A . F 3 NA 1 9 6 NA NA A . G 3 NA 1 10 8 NA NA A . H 3 NA 1 1 1 NA NA B . I 3 NA 1 2 2 NA NA B . J 3 NA 1 11 7 NA NA B . K 3 NA 1 12 9 NA NA B . L 3 NA 1 13 10 NA NA B . M 4 HOH 1 11 6 HOH HOH A . M 4 HOH 2 12 7 HOH HOH A . M 4 HOH 3 13 8 HOH HOH A . M 4 HOH 4 14 12 HOH HOH A . M 4 HOH 5 15 13 HOH HOH A . M 4 HOH 6 16 14 HOH HOH A . N 4 HOH 1 14 1 HOH HOH B . N 4 HOH 2 15 2 HOH HOH B . N 4 HOH 3 16 3 HOH HOH B . N 4 HOH 4 17 4 HOH HOH B . N 4 HOH 5 18 5 HOH HOH B . N 4 HOH 6 19 9 HOH HOH B . N 4 HOH 7 20 10 HOH HOH B . N 4 HOH 8 21 11 HOH HOH B . N 4 HOH 9 22 15 HOH HOH B . N 4 HOH 10 23 16 HOH HOH B . # _software.name LALS _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1PLY _cell.length_a 18.560 _cell.length_b 22.680 _cell.length_c 32.400 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 99.90 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PLY _symmetry.space_group_name_H-M 'P 1 1 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 # _exptl.entry_id 1PLY _exptl.method 'FIBER DIFFRACTION' _exptl.crystals_number ? # _refine.entry_id 1PLY _refine.ls_number_reflns_obs 102 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high 3.2 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2300000 _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _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 ;DUE TO THE LOW RESOLUTION OF THE DATA, THE THERMAL PARAMETER FOR ALL ATOMS WAS FIXED AT 4 ANGSTROMS**2. ; _refine.pdbx_starting_model ? _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.pdbx_refine_id 'FIBER DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 'FIBER DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 320 _refine_hist.pdbx_number_atoms_ligand 10 _refine_hist.number_atoms_solvent 16 _refine_hist.number_atoms_total 346 _refine_hist.d_res_high 3.2 _refine_hist.d_res_low . # _database_PDB_matrix.entry_id 1PLY _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 1PLY _struct.title 'SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1PLY _struct_keywords.pdbx_keywords DNA _struct_keywords.text DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 3 ? K N N 3 ? L N N 3 ? M N N 4 ? N N N 4 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1PLY 1PLY ? ? ? 2 2 PDB 1PLY 1PLY ? ? ? # 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 1PLY A 1 ? 5 ? 1PLY 1 ? 5 ? 1 5 2 2 1PLY B 1 ? 5 ? 1PLY 6 ? 10 ? 6 10 # _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,G,H,I,J,K,L,M,N # _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.details ;THE DNA IS A REGULAR TEN-FOLD HELIX HAVING TURN ANGLE 36 DEGREES AND AXIAL RISE 3.24 ANGSTROMS FOR EACH BASE-PAIR. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CORRESPONDS TO HALF THE UNIT CELL. IT CONTAINS HALF A TURN OF THE DNA HELIX I.E., 5 BASE PAIRS, 16 WATER MOLECULES AND 10 SODIUM IONS. THEY ARE IN AN ORTHOGONAL COORDINATE SYSTEM WHERE X IS PARALLEL TO A* AND Z IS PARALLEL TO C* (HELIX AXIS WHICH IS THE 2 SUB 1 AXIS OF THE SPACE GROUP SYMMETRY). ; _struct_biol.pdbx_parent_biol_id ? # 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 ? ? A DA 1 OP1 ? ? ? 1_555 E NA . NA ? ? A DA 1 A NA 8 1_555 ? ? ? ? ? ? ? 2.879 ? ? metalc2 metalc ? ? A DA 2 OP1 ? ? ? 1_555 D NA . NA ? ? A DA 2 A NA 7 1_555 ? ? ? ? ? ? ? 2.786 ? ? metalc3 metalc ? ? D NA . NA ? ? ? 1_555 M HOH . O ? ? A NA 7 A HOH 14 1_555 ? ? ? ? ? ? ? 2.642 ? ? metalc4 metalc ? ? E NA . NA ? ? ? 1_555 M HOH . O ? ? A NA 8 A HOH 15 1_555 ? ? ? ? ? ? ? 2.758 ? ? metalc5 metalc ? ? F NA . NA ? ? ? 1_555 M HOH . O ? ? A NA 9 A HOH 15 1_555 ? ? ? ? ? ? ? 2.912 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 1 B DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 1 B DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 2 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 2 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 3 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 3 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 4 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 4 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 1 N3 ? ? A DA 5 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 1 O4 ? ? A DA 5 B DT 6 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 OP1 ? A DA 1 ? A DA 1 ? 1_555 NA ? E NA . ? A NA 8 ? 1_555 O ? M HOH . ? A HOH 15 ? 1_555 96.2 ? 2 OP1 ? A DA 2 ? A DA 2 ? 1_555 NA ? D NA . ? A NA 7 ? 1_555 O ? M HOH . ? A HOH 14 ? 1_555 131.3 ? # 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 NA 1 ? 1 'BINDING SITE FOR RESIDUE NA B 1' AC2 Software B NA 2 ? 1 'BINDING SITE FOR RESIDUE NA B 2' AC3 Software A NA 7 ? 2 'BINDING SITE FOR RESIDUE NA A 7' AC4 Software A NA 8 ? 3 'BINDING SITE FOR RESIDUE NA A 8' AC5 Software A NA 9 ? 1 'BINDING SITE FOR RESIDUE NA A 9' AC6 Software B NA 11 ? 1 'BINDING SITE FOR RESIDUE NA B 11' AC7 Software A NA 10 ? 1 'BINDING SITE FOR RESIDUE NA A 10' AC8 Software B NA 12 ? 1 'BINDING SITE FOR RESIDUE NA B 12' AC9 Software B NA 13 ? 2 'BINDING SITE FOR RESIDUE NA B 13' # 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 1 DT B 5 ? DT B 10 . ? 1_555 ? 2 AC2 1 DT B 5 ? DT B 10 . ? 1_555 ? 3 AC3 2 DA A 2 ? DA A 2 . ? 1_555 ? 4 AC3 2 HOH M . ? HOH A 14 . ? 1_555 ? 5 AC4 3 DA A 1 ? DA A 1 . ? 1_555 ? 6 AC4 3 HOH M . ? HOH A 15 . ? 1_555 ? 7 AC4 3 DT B 5 ? DT B 10 . ? 1_545 ? 8 AC5 1 HOH M . ? HOH A 15 . ? 1_555 ? 9 AC6 1 DA A 5 ? DA A 5 . ? 1_545 ? 10 AC7 1 NA L . ? NA B 13 . ? 1_655 ? 11 AC8 1 DT B 4 ? DT B 9 . ? 1_555 ? 12 AC9 2 NA G . ? NA A 10 . ? 1_455 ? 13 AC9 2 DT B 2 ? DT B 7 . ? 1_555 ? # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 P A DA 1 ? ? 1_555 "O3'" A DA 5 ? ? 2_554 1.60 2 1 P B DT 6 ? ? 1_555 "O3'" B DT 10 ? ? 2_555 1.60 # 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 "C1'" A DA 1 ? ? "O4'" A DA 1 ? ? "C4'" A DA 1 ? ? 103.72 110.10 -6.38 1.00 N 2 1 "C3'" A DA 1 ? ? "C2'" A DA 1 ? ? "C1'" A DA 1 ? ? 92.74 102.40 -9.66 0.80 N 3 1 "C1'" A DA 2 ? ? "O4'" A DA 2 ? ? "C4'" A DA 2 ? ? 103.66 110.10 -6.44 1.00 N 4 1 "C3'" A DA 2 ? ? "C2'" A DA 2 ? ? "C1'" A DA 2 ? ? 92.75 102.40 -9.65 0.80 N 5 1 "C1'" A DA 3 ? ? "O4'" A DA 3 ? ? "C4'" A DA 3 ? ? 103.68 110.10 -6.42 1.00 N 6 1 "C3'" A DA 3 ? ? "C2'" A DA 3 ? ? "C1'" A DA 3 ? ? 92.73 102.40 -9.67 0.80 N 7 1 "C1'" A DA 4 ? ? "O4'" A DA 4 ? ? "C4'" A DA 4 ? ? 103.67 110.10 -6.43 1.00 N 8 1 "C3'" A DA 4 ? ? "C2'" A DA 4 ? ? "C1'" A DA 4 ? ? 92.72 102.40 -9.68 0.80 N 9 1 "C1'" A DA 5 ? ? "O4'" A DA 5 ? ? "C4'" A DA 5 ? ? 103.71 110.10 -6.39 1.00 N 10 1 "C3'" A DA 5 ? ? "C2'" A DA 5 ? ? "C1'" A DA 5 ? ? 92.76 102.40 -9.64 0.80 N 11 1 "C3'" B DT 6 ? ? "C2'" B DT 6 ? ? "C1'" B DT 6 ? ? 96.53 102.40 -5.87 0.80 N 12 1 "C3'" B DT 7 ? ? "C2'" B DT 7 ? ? "C1'" B DT 7 ? ? 96.51 102.40 -5.89 0.80 N 13 1 "C3'" B DT 8 ? ? "C2'" B DT 8 ? ? "C1'" B DT 8 ? ? 96.50 102.40 -5.90 0.80 N 14 1 "C3'" B DT 9 ? ? "C2'" B DT 9 ? ? "C1'" B DT 9 ? ? 96.55 102.40 -5.85 0.80 N 15 1 "C3'" B DT 10 ? ? "C2'" B DT 10 ? ? "C1'" B DT 10 ? ? 96.48 102.40 -5.92 0.80 N # 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 DT OP3 O N N 37 DT P P N N 38 DT OP1 O N N 39 DT OP2 O N N 40 DT "O5'" O N N 41 DT "C5'" C N N 42 DT "C4'" C N R 43 DT "O4'" O N N 44 DT "C3'" C N S 45 DT "O3'" O N N 46 DT "C2'" C N N 47 DT "C1'" C N R 48 DT N1 N N N 49 DT C2 C N N 50 DT O2 O N N 51 DT N3 N N N 52 DT C4 C N N 53 DT O4 O N N 54 DT C5 C N N 55 DT C7 C N N 56 DT C6 C N N 57 DT HOP3 H N N 58 DT HOP2 H N N 59 DT "H5'" H N N 60 DT "H5''" H N N 61 DT "H4'" H N N 62 DT "H3'" H N N 63 DT "HO3'" H N N 64 DT "H2'" H N N 65 DT "H2''" H N N 66 DT "H1'" H N N 67 DT H3 H N N 68 DT H71 H N N 69 DT H72 H N N 70 DT H73 H N N 71 DT H6 H N N 72 HOH O O N N 73 HOH H1 H N N 74 HOH H2 H N N 75 NA NA NA N N 76 # 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 DT OP3 P sing N N 39 DT OP3 HOP3 sing N N 40 DT P OP1 doub N N 41 DT P OP2 sing N N 42 DT P "O5'" sing N N 43 DT OP2 HOP2 sing N N 44 DT "O5'" "C5'" sing N N 45 DT "C5'" "C4'" sing N N 46 DT "C5'" "H5'" sing N N 47 DT "C5'" "H5''" sing N N 48 DT "C4'" "O4'" sing N N 49 DT "C4'" "C3'" sing N N 50 DT "C4'" "H4'" sing N N 51 DT "O4'" "C1'" sing N N 52 DT "C3'" "O3'" sing N N 53 DT "C3'" "C2'" sing N N 54 DT "C3'" "H3'" sing N N 55 DT "O3'" "HO3'" sing N N 56 DT "C2'" "C1'" sing N N 57 DT "C2'" "H2'" sing N N 58 DT "C2'" "H2''" sing N N 59 DT "C1'" N1 sing N N 60 DT "C1'" "H1'" sing N N 61 DT N1 C2 sing N N 62 DT N1 C6 sing N N 63 DT C2 O2 doub N N 64 DT C2 N3 sing N N 65 DT N3 C4 sing N N 66 DT N3 H3 sing N N 67 DT C4 O4 doub N N 68 DT C4 C5 sing N N 69 DT C5 C7 sing N N 70 DT C5 C6 doub N N 71 DT C7 H71 sing N N 72 DT C7 H72 sing N N 73 DT C7 H73 sing N N 74 DT C6 H6 sing N N 75 HOH O H1 sing N N 76 HOH O H2 sing N N 77 # _ndb_struct_conf_na.entry_id 1PLY _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 DA 1 1_555 B DT 5 1_555 0.032 -0.095 0.070 -0.035 -12.023 -1.868 1 A_DA1:DT10_B A 1 ? B 10 ? 20 1 1 A DA 2 1_555 B DT 4 1_555 0.032 -0.095 0.070 -0.043 -12.019 -1.863 2 A_DA2:DT9_B A 2 ? B 9 ? 20 1 1 A DA 3 1_555 B DT 3 1_555 0.032 -0.095 0.071 -0.025 -12.018 -1.874 3 A_DA3:DT8_B A 3 ? B 8 ? 20 1 1 A DA 4 1_555 B DT 2 1_555 0.031 -0.095 0.070 -0.019 -12.021 -1.863 4 A_DA4:DT7_B A 4 ? B 7 ? 20 1 1 A DA 5 1_555 B DT 1 1_555 0.032 -0.095 0.070 -0.040 -12.022 -1.868 5 A_DA5:DT6_B A 5 ? B 6 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DA 1 1_555 B DT 5 1_555 A DA 2 1_555 B DT 4 1_555 0.139 -0.341 3.219 1.071 -4.418 35.724 0.071 -0.074 3.240 -7.165 -1.737 36.002 1 AA_DA1DA2:DT9DT10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A DA 2 1_555 B DT 4 1_555 A DA 3 1_555 B DT 3 1_555 0.139 -0.342 3.219 1.085 -4.400 35.719 0.068 -0.071 3.239 -7.138 -1.760 35.996 2 AA_DA2DA3:DT8DT9_BB A 2 ? B 9 ? A 3 ? B 8 ? 1 A DA 3 1_555 B DT 3 1_555 A DA 4 1_555 B DT 2 1_555 0.139 -0.341 3.219 1.081 -4.409 35.721 0.069 -0.072 3.240 -7.151 -1.754 35.999 3 AA_DA3DA4:DT7DT8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A DA 4 1_555 B DT 2 1_555 A DA 5 1_555 B DT 1 1_555 0.139 -0.341 3.220 1.081 -4.420 35.727 0.071 -0.072 3.240 -7.168 -1.754 36.007 4 AA_DA4DA5:DT6DT7_BB A 4 ? B 7 ? A 5 ? B 6 ? # _atom_sites.entry_id 1PLY _atom_sites.fract_transf_matrix[1][1] 0.053879 _atom_sites.fract_transf_matrix[1][2] 0.009403 _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] 0.044758 _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] 0.030864 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N NA O P # loop_