data_1DN6 # _entry.id 1DN6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _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 1DN6 pdb_00001dn6 10.2210/pdb1dn6/pdb RCSB ADI009 ? ? WWPDB D_1000172851 ? ? # 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 1988-01-16 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' # 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 # 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' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DN6 _pdbx_database_status.recvd_initial_deposition_date 1987-05-11 _pdbx_database_status.deposit_site BNL _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 'McCall, M.' 1 'Brown, T.' 2 'Hunter, W.N.' 3 'Kennard, O.' 4 # _citation.id primary _citation.title 'The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA.' _citation.journal_abbrev Nature _citation.journal_volume 322 _citation.page_first 661 _citation.page_last 664 _citation.year 1986 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 3748146 _citation.pdbx_database_id_DOI 10.1038/322661a0 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'McCall, M.' 1 ? primary 'Brown, T.' 2 ? primary 'Hunter, W.N.' 3 ? primary 'Kennard, O.' 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 ;DNA (5'-D(*GP*GP*AP*TP*GP*GP*GP*AP*G)-3') ; 2860.884 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*TP*CP*CP*CP*AP*TP*CP*C)-3') ; 2611.726 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DG)(DG)(DA)(DT)(DG)(DG)(DG)(DA)(DG)' GGATGGGAG A ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DC)(DC)(DC)(DA)(DT)(DC)(DC)' CTCCCATCC B ? # 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 DA n 1 4 DT n 1 5 DG n 1 6 DG n 1 7 DG n 1 8 DA n 1 9 DG n 2 1 DC n 2 2 DT n 2 3 DC n 2 4 DC n 2 5 DC n 2 6 DA n 2 7 DT n 2 8 DC n 2 9 DC 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DG 9 9 9 DG G A . n B 2 1 DC 1 10 10 DC C B . n B 2 2 DT 2 11 11 DT T B . n B 2 3 DC 3 12 12 DC C B . n B 2 4 DC 4 13 13 DC C B . n B 2 5 DC 5 14 14 DC C B . n B 2 6 DA 6 15 15 DA A B . n B 2 7 DT 7 16 16 DT T B . n B 2 8 DC 8 17 17 DC C B . n B 2 9 DC 9 18 18 DC C B . n # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1DN6 _cell.length_a 45.290 _cell.length_b 45.290 _cell.length_c 24.730 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DN6 _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 # _exptl.entry_id 1DN6 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.32 _exptl_crystal.density_percent_sol 46.92 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 293.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'VAPOR DIFFUSION, temperature 293.00K' _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 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'MG ACETATE' ? ? ? 1 4 1 'NA CACODYLATE' ? ? ? 1 5 1 SPERMINE_HCL ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type ? _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 ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _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 1DN6 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 25.000 _reflns.d_resolution_high 2.700 _reflns.number_obs 1459 _reflns.number_all 1786 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1DN6 _refine.ls_number_reflns_obs 1032 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 3.000 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.3300000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _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 ? _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 'X-RAY 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 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 363 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 363 _refine_hist.d_res_high 3.000 _refine_hist.d_res_low 10.000 # 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 n_bond_d 0.022 ? ? ? 'X-RAY DIFFRACTION' ? n_angle_d 0.054 ? ? ? 'X-RAY DIFFRACTION' ? n_planar_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_bond_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_dihedral_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_impr_tor ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_plane_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1DN6 _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 1DN6 _struct.title 'THE CRYSTAL STRUCTURE OF D(GGATGGGAG). AN ESSENTIAL PART OF THE BINDING SITE FOR TRANSCRIPTION FACTOR IIIA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DN6 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'A-DNA, DOUBLE HELIX, 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 ? # 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 1DN6 1DN6 ? ? ? 2 2 PDB 1DN6 1DN6 ? ? ? # 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 1DN6 A 1 ? 9 ? 1DN6 1 ? 9 ? 1 9 2 2 1DN6 B 1 ? 9 ? 1DN6 10 ? 18 ? 10 18 # _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 # _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 # 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 DG 1 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 1 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 1 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 1 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 2 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 2 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 2 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 2 B DC 18 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog8 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 3 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 3 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 4 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 4 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 5 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 5 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 5 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 6 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 6 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 6 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 7 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 7 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 7 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 8 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 8 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 9 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 9 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 9 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DT 2 O4 ? ? A DG 9 B DT 11 1_555 ? ? ? ? ? ? 'DG-DT MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 "C5'" A DG 7 ? ? 1_555 C6 B DC 10 ? ? 3_654 1.86 2 1 "O3'" A DG 7 ? ? 1_555 N4 B DC 10 ? ? 3_654 1.91 3 1 "C4'" A DG 7 ? ? 1_555 C5 B DC 10 ? ? 3_654 1.92 4 1 "C4'" A DG 7 ? ? 1_555 C4 B DC 10 ? ? 3_654 2.04 # 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 "C2'" A DA 3 ? ? "C1'" A DA 3 ? ? 1.589 1.519 0.070 0.010 N 2 1 N9 A DA 3 ? ? C4 A DA 3 ? ? 1.415 1.374 0.041 0.006 N 3 1 "O4'" A DA 8 ? ? "C4'" A DA 8 ? ? 1.508 1.449 0.059 0.009 N 4 1 "C2'" B DC 10 ? ? "C1'" B DC 10 ? ? 1.650 1.519 0.131 0.010 N 5 1 "O4'" B DC 10 ? ? "C4'" B DC 10 ? ? 1.518 1.449 0.069 0.009 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 ? ? 116.26 108.30 7.96 0.30 N 2 1 N3 A DG 1 ? ? C2 A DG 1 ? ? N2 A DG 1 ? ? 124.27 119.90 4.37 0.70 N 3 1 "O3'" A DG 1 ? ? P A DG 2 ? ? OP1 A DG 2 ? ? 119.30 110.50 8.80 1.10 Y 4 1 OP1 A DG 2 ? ? P A DG 2 ? ? OP2 A DG 2 ? ? 109.88 119.60 -9.72 1.50 N 5 1 "C3'" A DG 2 ? ? "O3'" A DG 2 ? ? P A DA 3 ? ? 139.43 119.70 19.73 1.20 Y 6 1 "O4'" A DA 3 ? ? "C4'" A DA 3 ? ? "C3'" A DA 3 ? ? 100.76 104.50 -3.74 0.40 N 7 1 "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? "C3'" A DA 3 ? ? 125.26 115.70 9.56 1.20 N 8 1 "C4'" A DA 3 ? ? "C3'" A DA 3 ? ? "C2'" A DA 3 ? ? 93.70 102.20 -8.50 0.70 N 9 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 118.93 108.30 10.63 0.30 N 10 1 "C3'" A DA 3 ? ? "O3'" A DA 3 ? ? P A DT 4 ? ? 145.73 119.70 26.03 1.20 Y 11 1 "O3'" A DA 3 ? ? P A DT 4 ? ? OP1 A DT 4 ? ? 117.28 110.50 6.78 1.10 Y 12 1 "O5'" A DT 4 ? ? "C5'" A DT 4 ? ? "C4'" A DT 4 ? ? 102.28 109.40 -7.12 0.80 N 13 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 116.86 108.30 8.56 0.30 N 14 1 "O4'" A DG 5 ? ? "C4'" A DG 5 ? ? "C3'" A DG 5 ? ? 95.49 104.50 -9.01 0.40 N 15 1 "C5'" A DG 5 ? ? "C4'" A DG 5 ? ? "C3'" A DG 5 ? ? 127.39 115.70 11.69 1.20 N 16 1 "C1'" A DG 5 ? ? "O4'" A DG 5 ? ? "C4'" A DG 5 ? ? 100.93 110.10 -9.17 1.00 N 17 1 "C4'" A DG 5 ? ? "C3'" A DG 5 ? ? "O3'" A DG 5 ? ? 127.58 112.30 15.28 2.00 N 18 1 "C4'" A DG 5 ? ? "C3'" A DG 5 ? ? "C2'" A DG 5 ? ? 88.33 102.20 -13.87 0.70 N 19 1 "C3'" A DG 5 ? ? "C2'" A DG 5 ? ? "C1'" A DG 5 ? ? 96.52 102.40 -5.88 0.80 N 20 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 115.58 108.30 7.28 0.30 N 21 1 C8 A DG 5 ? ? N9 A DG 5 ? ? C4 A DG 5 ? ? 103.38 106.40 -3.02 0.40 N 22 1 N3 A DG 5 ? ? C2 A DG 5 ? ? N2 A DG 5 ? ? 115.40 119.90 -4.50 0.70 N 23 1 "C3'" A DG 5 ? ? "O3'" A DG 5 ? ? P A DG 6 ? ? 136.29 119.70 16.59 1.20 Y 24 1 "O5'" A DG 6 ? ? "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? 103.27 109.40 -6.13 0.80 N 25 1 "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? 108.58 103.10 5.48 0.90 N 26 1 "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? "C3'" A DG 7 ? ? 110.96 106.00 4.96 0.60 N 27 1 "C5'" A DG 7 ? ? "C4'" A DG 7 ? ? "O4'" A DG 7 ? ? 93.73 109.30 -15.57 1.90 N 28 1 "C1'" A DG 7 ? ? "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? 103.61 110.10 -6.49 1.00 N 29 1 "C4'" A DG 7 ? ? "C3'" A DG 7 ? ? "O3'" A DG 7 ? ? 126.86 112.30 14.56 2.00 N 30 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 117.52 108.30 9.22 0.30 N 31 1 "C3'" A DG 7 ? ? "O3'" A DG 7 ? ? P A DA 8 ? ? 127.08 119.70 7.38 1.20 Y 32 1 OP1 A DA 8 ? ? P A DA 8 ? ? OP2 A DA 8 ? ? 109.42 119.60 -10.18 1.50 N 33 1 "C1'" A DA 8 ? ? "O4'" A DA 8 ? ? "C4'" A DA 8 ? ? 99.95 110.10 -10.15 1.00 N 34 1 "C3'" A DA 8 ? ? "C2'" A DA 8 ? ? "C1'" A DA 8 ? ? 92.62 102.40 -9.78 0.80 N 35 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? "C2'" A DA 8 ? ? 98.06 105.90 -7.84 0.80 N 36 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 139.79 108.30 31.49 0.30 N 37 1 C8 A DA 8 ? ? N9 A DA 8 ? ? C4 A DA 8 ? ? 103.31 105.80 -2.49 0.40 N 38 1 P A DG 9 ? ? "O5'" A DG 9 ? ? "C5'" A DG 9 ? ? 130.66 120.90 9.76 1.60 N 39 1 "O4'" A DG 9 ? ? "C4'" A DG 9 ? ? "C3'" A DG 9 ? ? 109.87 106.00 3.87 0.60 N 40 1 "C1'" A DG 9 ? ? "O4'" A DG 9 ? ? "C4'" A DG 9 ? ? 103.95 110.10 -6.15 1.00 N 41 1 N1 A DG 9 ? ? C2 A DG 9 ? ? N2 A DG 9 ? ? 122.80 116.20 6.60 0.90 N 42 1 N3 A DG 9 ? ? C2 A DG 9 ? ? N2 A DG 9 ? ? 114.15 119.90 -5.75 0.70 N 43 1 N1 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 126.19 119.90 6.29 0.60 N 44 1 C5 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 123.49 128.60 -5.11 0.60 N 45 1 "C5'" B DC 10 ? ? "C4'" B DC 10 ? ? "C3'" B DC 10 ? ? 124.22 115.70 8.52 1.20 N 46 1 "C1'" B DC 10 ? ? "O4'" B DC 10 ? ? "C4'" B DC 10 ? ? 100.90 110.10 -9.20 1.00 N 47 1 "C4'" B DC 10 ? ? "C3'" B DC 10 ? ? "O3'" B DC 10 ? ? 130.71 112.30 18.41 2.00 N 48 1 "C4'" B DC 10 ? ? "C3'" B DC 10 ? ? "C2'" B DC 10 ? ? 93.98 102.20 -8.22 0.70 N 49 1 "C3'" B DC 10 ? ? "C2'" B DC 10 ? ? "C1'" B DC 10 ? ? 90.75 102.40 -11.65 0.80 N 50 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? "C2'" B DC 10 ? ? 94.45 105.90 -11.45 0.80 N 51 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? N1 B DC 10 ? ? 136.37 108.30 28.07 0.30 N 52 1 P B DT 11 ? ? "O5'" B DT 11 ? ? "C5'" B DT 11 ? ? 135.59 120.90 14.69 1.60 N 53 1 "C3'" B DT 11 ? ? "O3'" B DT 11 ? ? P B DC 12 ? ? 111.24 119.70 -8.46 1.20 Y 54 1 OP1 B DC 12 ? ? P B DC 12 ? ? OP2 B DC 12 ? ? 108.70 119.60 -10.90 1.50 N 55 1 P B DC 12 ? ? "O5'" B DC 12 ? ? "C5'" B DC 12 ? ? 135.03 120.90 14.13 1.60 N 56 1 "C5'" B DC 12 ? ? "C4'" B DC 12 ? ? "C3'" B DC 12 ? ? 123.35 115.70 7.65 1.20 N 57 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 112.83 108.30 4.53 0.30 N 58 1 P B DC 13 ? ? "O5'" B DC 13 ? ? "C5'" B DC 13 ? ? 141.68 120.90 20.78 1.60 N 59 1 "O4'" B DC 13 ? ? "C1'" B DC 13 ? ? N1 B DC 13 ? ? 121.81 108.30 13.51 0.30 N 60 1 OP1 B DC 14 ? ? P B DC 14 ? ? OP2 B DC 14 ? ? 107.83 119.60 -11.77 1.50 N 61 1 "O4'" B DC 14 ? ? "C4'" B DC 14 ? ? "C3'" B DC 14 ? ? 99.26 104.50 -5.24 0.40 N 62 1 "C5'" B DC 14 ? ? "C4'" B DC 14 ? ? "O4'" B DC 14 ? ? 121.57 109.80 11.77 1.10 N 63 1 "C4'" B DC 14 ? ? "C3'" B DC 14 ? ? "C2'" B DC 14 ? ? 95.14 102.20 -7.06 0.70 N 64 1 "O4'" B DC 14 ? ? "C1'" B DC 14 ? ? N1 B DC 14 ? ? 118.65 108.30 10.35 0.30 N 65 1 C6 B DC 14 ? ? N1 B DC 14 ? ? C2 B DC 14 ? ? 117.45 120.30 -2.85 0.40 N 66 1 C5 B DC 14 ? ? C6 B DC 14 ? ? N1 B DC 14 ? ? 124.24 121.00 3.24 0.50 N 67 1 "C3'" B DC 14 ? ? "O3'" B DC 14 ? ? P B DA 15 ? ? 127.25 119.70 7.55 1.20 Y 68 1 "O5'" B DA 15 ? ? "C5'" B DA 15 ? ? "C4'" B DA 15 ? ? 102.33 109.40 -7.07 0.80 N 69 1 "C4'" B DA 15 ? ? "C3'" B DA 15 ? ? "C2'" B DA 15 ? ? 96.50 102.20 -5.70 0.70 N 70 1 "O4'" B DA 15 ? ? "C1'" B DA 15 ? ? N9 B DA 15 ? ? 111.26 108.30 2.96 0.30 N 71 1 "C3'" B DA 15 ? ? "O3'" B DA 15 ? ? P B DT 16 ? ? 131.57 119.70 11.87 1.20 Y 72 1 "O3'" B DA 15 ? ? P B DT 16 ? ? OP1 B DT 16 ? ? 118.88 110.50 8.38 1.10 Y 73 1 "O5'" B DT 16 ? ? "C5'" B DT 16 ? ? "C4'" B DT 16 ? ? 100.70 109.40 -8.70 0.80 N 74 1 "O4'" B DT 16 ? ? "C4'" B DT 16 ? ? "C3'" B DT 16 ? ? 109.90 106.00 3.90 0.60 N 75 1 "C4'" B DT 16 ? ? "C3'" B DT 16 ? ? "O3'" B DT 16 ? ? 124.86 112.30 12.56 2.00 N 76 1 "O4'" B DT 16 ? ? "C1'" B DT 16 ? ? N1 B DT 16 ? ? 121.91 108.30 13.61 0.30 N 77 1 N3 B DT 16 ? ? C2 B DT 16 ? ? O2 B DT 16 ? ? 116.49 122.30 -5.81 0.60 N 78 1 OP1 B DC 18 ? ? P B DC 18 ? ? OP2 B DC 18 ? ? 107.28 119.60 -12.32 1.50 N 79 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? N1 B DC 18 ? ? 128.92 108.30 20.62 0.30 N 80 1 C5 B DC 18 ? ? C4 B DC 18 ? ? N4 B DC 18 ? ? 125.62 120.20 5.42 0.70 N # _refine_B_iso.class 'ALL ATOMS' _refine_B_iso.details TF _refine_B_iso.treatment isotropic _refine_B_iso.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_occupancy.class 'ALL ATOMS' _refine_occupancy.treatment fix _refine_occupancy.pdbx_refine_id 'X-RAY DIFFRACTION' # 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 # 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 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1DN6 'double helix' 1DN6 'a-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 DG 1 1_555 B DC 9 1_555 0.955 0.170 -0.288 -8.087 -23.810 0.763 1 A_DG1:DC18_B A 1 ? B 18 ? 19 1 1 A DG 2 1_555 B DC 8 1_555 -1.250 -0.662 0.352 18.850 12.535 -9.105 2 A_DG2:DC17_B A 2 ? B 17 ? 19 1 1 A DA 3 1_555 B DT 7 1_555 -1.153 -0.216 -0.583 -13.211 -3.874 -0.683 3 A_DA3:DT16_B A 3 ? B 16 ? 20 1 1 A DT 4 1_555 B DA 6 1_555 -0.193 -0.013 -0.020 -17.333 7.747 -5.557 4 A_DT4:DA15_B A 4 ? B 15 ? 20 1 1 A DG 5 1_555 B DC 5 1_555 -0.316 -0.615 1.037 5.252 -8.105 -3.588 5 A_DG5:DC14_B A 5 ? B 14 ? 19 1 1 A DG 6 1_555 B DC 4 1_555 0.075 -0.174 -0.381 12.565 18.229 -7.286 6 A_DG6:DC13_B A 6 ? B 13 ? 19 1 1 A DG 7 1_555 B DC 3 1_555 0.874 -0.334 -0.741 -8.543 7.577 -12.338 7 A_DG7:DC12_B A 7 ? B 12 ? 19 1 1 A DA 8 1_555 B DT 2 1_555 -0.855 -0.390 -0.092 -1.060 16.805 -26.188 8 A_DA8:DT11_B A 8 ? B 11 ? 20 1 1 A DG 9 1_555 B DC 1 1_555 2.002 -0.600 -0.910 14.453 14.482 -11.189 9 A_DG9:DC10_B A 9 ? B 10 ? 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 DG 1 1_555 B DC 9 1_555 A DG 2 1_555 B DC 8 1_555 0.380 -0.586 2.279 -1.995 3.848 16.875 -3.521 -2.076 2.037 12.839 6.656 17.419 1 AA_DG1DG2:DC17DC18_BB A 1 ? B 18 ? A 2 ? B 17 ? 1 A DG 2 1_555 B DC 8 1_555 A DA 3 1_555 B DT 7 1_555 1.300 -1.423 4.028 0.610 26.753 35.042 -4.734 -1.677 2.426 38.302 -0.873 43.835 2 AA_DG2DA3:DT16DC17_BB A 2 ? B 17 ? A 3 ? B 16 ? 1 A DA 3 1_555 B DT 7 1_555 A DT 4 1_555 B DA 6 1_555 -1.130 -1.288 3.488 -5.299 7.789 35.373 -3.182 1.033 3.271 12.546 8.535 36.567 3 AA_DA3DT4:DA15DT16_BB A 3 ? B 16 ? A 4 ? B 15 ? 1 A DT 4 1_555 B DA 6 1_555 A DG 5 1_555 B DC 5 1_555 0.133 -2.263 2.209 -9.083 6.463 14.951 -8.843 -3.017 0.930 21.377 30.044 18.630 4 AA_DT4DG5:DC14DA15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A DG 5 1_555 B DC 5 1_555 A DG 6 1_555 B DC 4 1_555 -0.232 -1.687 3.086 9.626 -11.348 39.096 -1.162 1.349 3.289 -16.259 -13.793 41.729 5 AA_DG5DG6:DC13DC14_BB A 5 ? B 14 ? A 6 ? B 13 ? 1 A DG 6 1_555 B DC 4 1_555 A DG 7 1_555 B DC 3 1_555 0.319 -2.720 4.651 3.667 18.832 30.050 -7.772 0.123 2.575 32.492 -6.327 35.533 6 AA_DG6DG7:DC12DC13_BB A 6 ? B 13 ? A 7 ? B 12 ? 1 A DG 7 1_555 B DC 3 1_555 A DA 8 1_555 B DT 2 1_555 -0.308 -1.503 2.941 -6.507 2.023 18.379 -5.293 -1.914 2.708 6.069 19.525 19.591 7 AA_DG7DA8:DT11DC12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A DA 8 1_555 B DT 2 1_555 A DG 9 1_555 B DC 1 1_555 1.036 -1.557 2.799 1.814 -5.359 61.018 -1.305 -0.941 2.940 -5.266 -1.783 61.255 8 AA_DA8DG9:DC10DT11_BB A 8 ? B 11 ? A 9 ? B 10 ? # _atom_sites.entry_id 1DN6 _atom_sites.fract_transf_matrix[1][1] 0.022080 _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] 0.022080 _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] 0.040437 _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_