data_404D # _entry.id 404D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 404D pdb_0000404d 10.2210/pdb404d/pdb NDB AH0001 ? ? RCSB RCSB000265 ? ? WWPDB D_1000000265 ? ? # 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 1998-12-14 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-01-24 5 'Structure model' 1 4 2023-12-27 # _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' 'Structure summary' 4 5 'Structure model' 'Data collection' 5 5 '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' audit_author 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 '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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 404D _pdbx_database_status.recvd_initial_deposition_date 1998-06-12 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site RCSB _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Conn, G.' 1 ? 'Brown, T.' 2 ? 'Leonard, G.A.' 3 ? # _citation.id primary _citation.title 'The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) shows significant differences to that found in solution.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 27 _citation.page_first 555 _citation.page_last 561 _citation.year 1999 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9862980 _citation.pdbx_database_id_DOI 10.1093/nar/27.2.555 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Conn, G.L.' 1 ? primary 'Brown, T.' 2 ? primary 'Leonard, G.A.' 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 "5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'" 3287.076 1 ? ? ? ? 2 polymer syn "5'-D(*GP*CP*TP*TP*CP*TP*CP*TP*TP*C)-3'" 2961.940 1 ? ? ? ? 3 water nat water 18.015 9 ? ? ? ? # 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 polyribonucleotide no no GAAGAGAAGC GAAGAGAAGC A ? 2 polydeoxyribonucleotide no no '(DG)(DC)(DT)(DT)(DC)(DT)(DC)(DT)(DT)(DC)' GCTTCTCTTC B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 A n 1 3 A n 1 4 G n 1 5 A n 1 6 G n 1 7 A n 1 8 A n 1 9 G n 1 10 C n 2 1 DG n 2 2 DC n 2 3 DT n 2 4 DT n 2 5 DC n 2 6 DT n 2 7 DC n 2 8 DT n 2 9 DT n 2 10 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 G 1 1 1 G G A . n A 1 2 A 2 2 2 A A A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 G 6 6 6 G G A . n A 1 7 A 7 7 7 A A A . n A 1 8 A 8 8 8 A A A . n A 1 9 G 9 9 9 G G A . n A 1 10 C 10 10 10 C C A . n B 2 1 DG 1 11 11 DG G B . n B 2 2 DC 2 12 12 DC C B . n B 2 3 DT 3 13 13 DT T B . n B 2 4 DT 4 14 14 DT T B . n B 2 5 DC 5 15 15 DC C B . n B 2 6 DT 6 16 16 DT T B . n B 2 7 DC 7 17 17 DC C B . n B 2 8 DT 8 18 18 DT T B . n B 2 9 DT 9 19 19 DT T B . n B 2 10 DC 10 20 20 DC C 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 HOH 1 23 23 HOH HOH A . C 3 HOH 2 24 24 HOH HOH A . C 3 HOH 3 25 25 HOH HOH A . C 3 HOH 4 27 27 HOH HOH A . C 3 HOH 5 29 29 HOH HOH A . D 3 HOH 1 21 21 HOH HOH B . D 3 HOH 2 22 22 HOH HOH B . D 3 HOH 3 26 26 HOH HOH B . D 3 HOH 4 28 28 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 . ? 3 # _cell.entry_id 404D _cell.length_a 25.720 _cell.length_b 45.550 _cell.length_c 47.810 _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 404D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 # _exptl.entry_id 404D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 44.41 _exptl_crystal.density_Matthews 2.21 _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 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, 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 HEPES ? ? ? 1 2 1 PEG4000 ? ? ? 1 3 1 'AMMONIUM ACETATE' ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 2 HEPES ? ? ? 1 6 2 PEG4000 ? ? ? 1 7 2 'AMMONIUM ACETATE' ? ? ? 1 8 2 MGCL2 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 293.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'PRINCETON 2K' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 404D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F 0.000 _reflns.d_resolution_low 30.000 _reflns.d_resolution_high 2.500 _reflns.number_obs 1881 _reflns.number_all 1881 _reflns.percent_possible_obs 86.600 _reflns.pdbx_Rmerge_I_obs 0.056 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.060 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 404D _refine.ls_number_reflns_obs 1867 _refine.ls_number_reflns_all 1867 _refine.pdbx_ls_sigma_I 0.000 _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 20.000 _refine.ls_d_res_high 2.500 _refine.ls_percent_reflns_obs 86.600 _refine.ls_R_factor_obs 0.181 _refine.ls_R_factor_all 0.181 _refine.ls_R_factor_R_work 0.184 _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.ls_redundancy_reflns_obs ? _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.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 414 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 9 _refine_hist.number_atoms_total 423 _refine_hist.d_res_high 2.500 _refine_hist.d_res_low 20.000 # _database_PDB_matrix.entry_id 404D _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 404D _struct.title 'CRYSTAL STRUCTURE OF THE RNA/DNA HYBRID R(GAAGAGAAGC). D(GCTTCTCTTC)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 404D _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'RNA/DNA HYBRID R(GAAGAGAAGC).D(GCTTCTCTTC), DNA-RNA COMPLEX, DNA-RNA HYBRID' # 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 ? # 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 404D 404D ? ? ? 2 2 PDB 404D 404D ? ? ? # 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 404D A 1 ? 10 ? 404D 1 ? 10 ? 1 10 2 2 404D B 1 ? 10 ? 404D 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 G 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A G 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A G 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A G 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N1 ? ? ? 1_555 B DT 9 N3 ? ? A A 2 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 2 N6 ? ? ? 1_555 B DT 9 O4 ? ? A A 2 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N1 ? ? ? 1_555 B DT 8 N3 ? ? A A 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N6 ? ? ? 1_555 B DT 8 O4 ? ? A A 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A G 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A G 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A G 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 B DT 6 N3 ? ? A A 5 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 B DT 6 O4 ? ? A A 5 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 N1 ? ? ? 1_555 B DC 5 N3 ? ? A G 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N2 ? ? ? 1_555 B DC 5 O2 ? ? A G 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 O6 ? ? ? 1_555 B DC 5 N4 ? ? A G 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A A 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A A 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N1 ? ? ? 1_555 B DT 3 N3 ? ? A A 8 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 8 N6 ? ? ? 1_555 B DT 3 O4 ? ? A A 8 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A G 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A G 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A G 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A C 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A C 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A C 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 C5 B DC 17 ? ? C6 B DC 17 ? ? 1.389 1.339 0.050 0.008 N 2 1 C6 B DT 19 ? ? N1 B DT 19 ? ? 1.335 1.378 -0.043 0.007 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 "O5'" A G 1 ? ? "C5'" A G 1 ? ? "C4'" A G 1 ? ? 103.35 109.40 -6.05 0.80 N 2 1 C2 A G 1 ? ? N3 A G 1 ? ? C4 A G 1 ? ? 115.16 111.90 3.26 0.50 N 3 1 C6 A A 3 ? ? N1 A A 3 ? ? C2 A A 3 ? ? 124.17 118.60 5.57 0.60 N 4 1 C5 A A 3 ? ? C6 A A 3 ? ? N1 A A 3 ? ? 113.75 117.70 -3.95 0.50 N 5 1 N3 A A 3 ? ? C4 A A 3 ? ? N9 A A 3 ? ? 122.37 127.40 -5.03 0.80 N 6 1 "C3'" A A 3 ? ? "O3'" A A 3 ? ? P A G 4 ? ? 129.02 119.70 9.32 1.20 Y 7 1 "O5'" A G 4 ? ? "C5'" A G 4 ? ? "C4'" A G 4 ? ? 100.05 109.40 -9.35 0.80 N 8 1 "C3'" A G 4 ? ? "C2'" A G 4 ? ? "C1'" A G 4 ? ? 96.00 101.30 -5.30 0.70 N 9 1 C6 A G 4 ? ? N1 A G 4 ? ? C2 A G 4 ? ? 128.80 125.10 3.70 0.60 N 10 1 N1 A G 4 ? ? C2 A G 4 ? ? N3 A G 4 ? ? 119.86 123.90 -4.04 0.60 N 11 1 "O4'" A A 5 ? ? "C4'" A A 5 ? ? "C3'" A A 5 ? ? 97.63 104.00 -6.37 1.00 N 12 1 "C5'" A A 5 ? ? "C4'" A A 5 ? ? "O4'" A A 5 ? ? 115.33 109.80 5.53 0.90 N 13 1 "C3'" A A 5 ? ? "C2'" A A 5 ? ? "C1'" A A 5 ? ? 95.97 101.30 -5.33 0.70 N 14 1 "O4'" A A 5 ? ? "C1'" A A 5 ? ? N9 A A 5 ? ? 100.76 108.20 -7.44 0.80 N 15 1 N1 A A 5 ? ? C2 A A 5 ? ? N3 A A 5 ? ? 125.92 129.30 -3.38 0.50 N 16 1 "O5'" A G 6 ? ? "C5'" A G 6 ? ? "C4'" A G 6 ? ? 102.66 109.40 -6.74 0.80 N 17 1 P A G 6 ? ? "O5'" A G 6 ? ? "C5'" A G 6 ? ? 111.02 120.90 -9.88 1.60 N 18 1 "C5'" A G 6 ? ? "C4'" A G 6 ? ? "C3'" A G 6 ? ? 106.47 115.20 -8.73 1.40 N 19 1 "C3'" A G 6 ? ? "C2'" A G 6 ? ? "C1'" A G 6 ? ? 96.80 101.30 -4.50 0.70 N 20 1 "O4'" A G 6 ? ? "C1'" A G 6 ? ? N9 A G 6 ? ? 113.94 108.50 5.44 0.70 N 21 1 C8 A G 6 ? ? N9 A G 6 ? ? "C1'" A G 6 ? ? 135.88 127.00 8.88 1.30 N 22 1 "O5'" A A 8 ? ? "C5'" A A 8 ? ? "C4'" A A 8 ? ? 100.63 109.40 -8.77 0.80 N 23 1 C6 A A 8 ? ? N1 A A 8 ? ? C2 A A 8 ? ? 122.32 118.60 3.72 0.60 N 24 1 N1 A A 8 ? ? C2 A A 8 ? ? N3 A A 8 ? ? 125.69 129.30 -3.61 0.50 N 25 1 N7 A A 8 ? ? C8 A A 8 ? ? N9 A A 8 ? ? 110.16 113.80 -3.64 0.50 N 26 1 C8 A A 8 ? ? N9 A A 8 ? ? C4 A A 8 ? ? 109.43 105.80 3.63 0.40 N 27 1 "O5'" A G 9 ? ? "C5'" A G 9 ? ? "C4'" A G 9 ? ? 104.43 109.40 -4.97 0.80 N 28 1 N3 A C 10 ? ? C4 A C 10 ? ? N4 A C 10 ? ? 113.46 118.00 -4.54 0.70 N 29 1 "O4'" B DG 11 ? ? "C4'" B DG 11 ? ? "C3'" B DG 11 ? ? 97.47 104.50 -7.03 0.40 N 30 1 "C3'" B DG 11 ? ? "C2'" B DG 11 ? ? "C1'" B DG 11 ? ? 96.60 102.40 -5.80 0.80 N 31 1 "O4'" B DC 12 ? ? "C4'" B DC 12 ? ? "C3'" B DC 12 ? ? 98.60 104.50 -5.90 0.40 N 32 1 "C3'" B DC 12 ? ? "C2'" B DC 12 ? ? "C1'" B DC 12 ? ? 93.21 102.40 -9.19 0.80 N 33 1 C2 B DC 12 ? ? N3 B DC 12 ? ? C4 B DC 12 ? ? 123.26 119.90 3.36 0.50 N 34 1 "C3'" B DC 12 ? ? "O3'" B DC 12 ? ? P B DT 13 ? ? 128.16 119.70 8.46 1.20 Y 35 1 "O4'" B DT 13 ? ? "C4'" B DT 13 ? ? "C3'" B DT 13 ? ? 97.21 104.50 -7.29 0.40 N 36 1 "C3'" B DT 13 ? ? "C2'" B DT 13 ? ? "C1'" B DT 13 ? ? 96.35 102.40 -6.05 0.80 N 37 1 C5 B DT 13 ? ? C6 B DT 13 ? ? N1 B DT 13 ? ? 118.86 123.70 -4.84 0.60 N 38 1 N3 B DT 13 ? ? C4 B DT 13 ? ? O4 B DT 13 ? ? 114.63 119.90 -5.27 0.60 N 39 1 C5 B DT 13 ? ? C4 B DT 13 ? ? O4 B DT 13 ? ? 130.85 124.90 5.95 0.70 N 40 1 "C3'" B DT 13 ? ? "O3'" B DT 13 ? ? P B DT 14 ? ? 126.90 119.70 7.20 1.20 Y 41 1 "O4'" B DT 14 ? ? "C4'" B DT 14 ? ? "C3'" B DT 14 ? ? 100.72 104.50 -3.78 0.40 N 42 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 103.59 108.00 -4.41 0.70 N 43 1 C5 B DT 14 ? ? C6 B DT 14 ? ? N1 B DT 14 ? ? 120.01 123.70 -3.69 0.60 N 44 1 "O4'" B DC 15 ? ? "C4'" B DC 15 ? ? "C3'" B DC 15 ? ? 96.98 104.50 -7.52 0.40 N 45 1 "C3'" B DC 15 ? ? "C2'" B DC 15 ? ? "C1'" B DC 15 ? ? 96.83 102.40 -5.57 0.80 N 46 1 "O4'" B DT 16 ? ? "C4'" B DT 16 ? ? "C3'" B DT 16 ? ? 96.47 104.50 -8.03 0.40 N 47 1 "C3'" B DT 16 ? ? "C2'" B DT 16 ? ? "C1'" B DT 16 ? ? 96.30 102.40 -6.10 0.80 N 48 1 C6 B DT 16 ? ? C5 B DT 16 ? ? C7 B DT 16 ? ? 117.68 122.90 -5.22 0.60 N 49 1 "O4'" B DC 17 ? ? "C4'" B DC 17 ? ? "C3'" B DC 17 ? ? 100.01 104.50 -4.49 0.40 N 50 1 N3 B DC 17 ? ? C4 B DC 17 ? ? N4 B DC 17 ? ? 110.24 118.00 -7.76 0.70 N 51 1 C5 B DC 17 ? ? C4 B DC 17 ? ? N4 B DC 17 ? ? 128.40 120.20 8.20 0.70 N 52 1 C2 B DC 17 ? ? N1 B DC 17 ? ? "C1'" B DC 17 ? ? 111.03 118.80 -7.77 1.10 N 53 1 "C3'" B DC 17 ? ? "O3'" B DC 17 ? ? P B DT 18 ? ? 131.76 119.70 12.06 1.20 Y 54 1 "O4'" B DT 18 ? ? "C4'" B DT 18 ? ? "C3'" B DT 18 ? ? 99.79 104.50 -4.71 0.40 N 55 1 N3 B DT 18 ? ? C2 B DT 18 ? ? O2 B DT 18 ? ? 117.87 122.30 -4.43 0.60 N 56 1 C4 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 114.00 119.00 -5.00 0.60 N 57 1 "C3'" B DT 18 ? ? "O3'" B DT 18 ? ? P B DT 19 ? ? 131.51 119.70 11.81 1.20 Y 58 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 103.03 108.00 -4.97 0.70 N 59 1 C2 B DT 19 ? ? N3 B DT 19 ? ? C4 B DT 19 ? ? 122.67 127.20 -4.53 0.60 N 60 1 C4 B DT 19 ? ? C5 B DT 19 ? ? C6 B DT 19 ? ? 122.52 118.00 4.52 0.60 N 61 1 C5 B DT 19 ? ? C6 B DT 19 ? ? N1 B DT 19 ? ? 117.91 123.70 -5.79 0.60 N 62 1 N1 B DT 19 ? ? C2 B DT 19 ? ? O2 B DT 19 ? ? 113.26 123.10 -9.84 0.80 N 63 1 N3 B DT 19 ? ? C2 B DT 19 ? ? O2 B DT 19 ? ? 129.47 122.30 7.17 0.60 N 64 1 C6 B DT 19 ? ? C5 B DT 19 ? ? C7 B DT 19 ? ? 115.60 122.90 -7.30 0.60 N 65 1 "O4'" B DC 20 ? ? "C1'" B DC 20 ? ? N1 B DC 20 ? ? 112.85 108.30 4.55 0.30 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 DG OP3 O N N 107 DG P P N N 108 DG OP1 O N N 109 DG OP2 O N N 110 DG "O5'" O N N 111 DG "C5'" C N N 112 DG "C4'" C N R 113 DG "O4'" O N N 114 DG "C3'" C N S 115 DG "O3'" O N N 116 DG "C2'" C N N 117 DG "C1'" C N R 118 DG N9 N Y N 119 DG C8 C Y N 120 DG N7 N Y N 121 DG C5 C Y N 122 DG C6 C N N 123 DG O6 O N N 124 DG N1 N N N 125 DG C2 C N N 126 DG N2 N N N 127 DG N3 N N N 128 DG C4 C Y N 129 DG HOP3 H N N 130 DG HOP2 H N N 131 DG "H5'" H N N 132 DG "H5''" H N N 133 DG "H4'" H N N 134 DG "H3'" H N N 135 DG "HO3'" H N N 136 DG "H2'" H N N 137 DG "H2''" H N N 138 DG "H1'" H N N 139 DG H8 H N N 140 DG H1 H N N 141 DG H21 H N N 142 DG H22 H N N 143 DT OP3 O N N 144 DT P P N N 145 DT OP1 O N N 146 DT OP2 O N N 147 DT "O5'" O N N 148 DT "C5'" C N N 149 DT "C4'" C N R 150 DT "O4'" O N N 151 DT "C3'" C N S 152 DT "O3'" O N N 153 DT "C2'" C N N 154 DT "C1'" C N R 155 DT N1 N N N 156 DT C2 C N N 157 DT O2 O N N 158 DT N3 N N N 159 DT C4 C N N 160 DT O4 O N N 161 DT C5 C N N 162 DT C7 C N N 163 DT C6 C N N 164 DT HOP3 H N N 165 DT HOP2 H N N 166 DT "H5'" H N N 167 DT "H5''" H N N 168 DT "H4'" H N N 169 DT "H3'" H N N 170 DT "HO3'" H N N 171 DT "H2'" H N N 172 DT "H2''" H N N 173 DT "H1'" H N N 174 DT H3 H N N 175 DT H71 H N N 176 DT H72 H N N 177 DT H73 H N N 178 DT H6 H N N 179 G OP3 O N N 180 G P P N N 181 G OP1 O N N 182 G OP2 O N N 183 G "O5'" O N N 184 G "C5'" C N N 185 G "C4'" C N R 186 G "O4'" O N N 187 G "C3'" C N S 188 G "O3'" O N N 189 G "C2'" C N R 190 G "O2'" O N N 191 G "C1'" C N R 192 G N9 N Y N 193 G C8 C Y N 194 G N7 N Y N 195 G C5 C Y N 196 G C6 C N N 197 G O6 O N N 198 G N1 N N N 199 G C2 C N N 200 G N2 N N N 201 G N3 N N N 202 G C4 C Y N 203 G HOP3 H N N 204 G HOP2 H N N 205 G "H5'" H N N 206 G "H5''" H N N 207 G "H4'" H N N 208 G "H3'" H N N 209 G "HO3'" H N N 210 G "H2'" H N N 211 G "HO2'" H N N 212 G "H1'" H N N 213 G H8 H N N 214 G H1 H N N 215 G H21 H N N 216 G H22 H N N 217 HOH O O N N 218 HOH H1 H N N 219 HOH H2 H N N 220 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 DG OP3 P sing N N 111 DG OP3 HOP3 sing N N 112 DG P OP1 doub N N 113 DG P OP2 sing N N 114 DG P "O5'" sing N N 115 DG OP2 HOP2 sing N N 116 DG "O5'" "C5'" sing N N 117 DG "C5'" "C4'" sing N N 118 DG "C5'" "H5'" sing N N 119 DG "C5'" "H5''" sing N N 120 DG "C4'" "O4'" sing N N 121 DG "C4'" "C3'" sing N N 122 DG "C4'" "H4'" sing N N 123 DG "O4'" "C1'" sing N N 124 DG "C3'" "O3'" sing N N 125 DG "C3'" "C2'" sing N N 126 DG "C3'" "H3'" sing N N 127 DG "O3'" "HO3'" sing N N 128 DG "C2'" "C1'" sing N N 129 DG "C2'" "H2'" sing N N 130 DG "C2'" "H2''" sing N N 131 DG "C1'" N9 sing N N 132 DG "C1'" "H1'" sing N N 133 DG N9 C8 sing Y N 134 DG N9 C4 sing Y N 135 DG C8 N7 doub Y N 136 DG C8 H8 sing N N 137 DG N7 C5 sing Y N 138 DG C5 C6 sing N N 139 DG C5 C4 doub Y N 140 DG C6 O6 doub N N 141 DG C6 N1 sing N N 142 DG N1 C2 sing N N 143 DG N1 H1 sing N N 144 DG C2 N2 sing N N 145 DG C2 N3 doub N N 146 DG N2 H21 sing N N 147 DG N2 H22 sing N N 148 DG N3 C4 sing N N 149 DT OP3 P sing N N 150 DT OP3 HOP3 sing N N 151 DT P OP1 doub N N 152 DT P OP2 sing N N 153 DT P "O5'" sing N N 154 DT OP2 HOP2 sing N N 155 DT "O5'" "C5'" sing N N 156 DT "C5'" "C4'" sing N N 157 DT "C5'" "H5'" sing N N 158 DT "C5'" "H5''" sing N N 159 DT "C4'" "O4'" sing N N 160 DT "C4'" "C3'" sing N N 161 DT "C4'" "H4'" sing N N 162 DT "O4'" "C1'" sing N N 163 DT "C3'" "O3'" sing N N 164 DT "C3'" "C2'" sing N N 165 DT "C3'" "H3'" sing N N 166 DT "O3'" "HO3'" sing N N 167 DT "C2'" "C1'" sing N N 168 DT "C2'" "H2'" sing N N 169 DT "C2'" "H2''" sing N N 170 DT "C1'" N1 sing N N 171 DT "C1'" "H1'" sing N N 172 DT N1 C2 sing N N 173 DT N1 C6 sing N N 174 DT C2 O2 doub N N 175 DT C2 N3 sing N N 176 DT N3 C4 sing N N 177 DT N3 H3 sing N N 178 DT C4 O4 doub N N 179 DT C4 C5 sing N N 180 DT C5 C7 sing N N 181 DT C5 C6 doub N N 182 DT C7 H71 sing N N 183 DT C7 H72 sing N N 184 DT C7 H73 sing N N 185 DT C6 H6 sing N N 186 G OP3 P sing N N 187 G OP3 HOP3 sing N N 188 G P OP1 doub N N 189 G P OP2 sing N N 190 G P "O5'" sing N N 191 G OP2 HOP2 sing N N 192 G "O5'" "C5'" sing N N 193 G "C5'" "C4'" sing N N 194 G "C5'" "H5'" sing N N 195 G "C5'" "H5''" sing N N 196 G "C4'" "O4'" sing N N 197 G "C4'" "C3'" sing N N 198 G "C4'" "H4'" sing N N 199 G "O4'" "C1'" sing N N 200 G "C3'" "O3'" sing N N 201 G "C3'" "C2'" sing N N 202 G "C3'" "H3'" sing N N 203 G "O3'" "HO3'" sing N N 204 G "C2'" "O2'" sing N N 205 G "C2'" "C1'" sing N N 206 G "C2'" "H2'" sing N N 207 G "O2'" "HO2'" sing N N 208 G "C1'" N9 sing N N 209 G "C1'" "H1'" sing N N 210 G N9 C8 sing Y N 211 G N9 C4 sing Y N 212 G C8 N7 doub Y N 213 G C8 H8 sing N N 214 G N7 C5 sing Y N 215 G C5 C6 sing N N 216 G C5 C4 doub Y N 217 G C6 O6 doub N N 218 G C6 N1 sing N N 219 G N1 C2 sing N N 220 G N1 H1 sing N N 221 G C2 N2 sing N N 222 G C2 N3 doub N N 223 G N2 H21 sing N N 224 G N2 H22 sing N N 225 G N3 C4 sing N N 226 HOH O H1 sing N N 227 HOH O H2 sing N N 228 # _ndb_struct_conf_na.entry_id 404D _ndb_struct_conf_na.feature '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 G 1 1_555 B DC 10 1_555 -0.120 -0.240 -0.132 -10.146 -3.654 -1.631 1 A_G1:DC20_B A 1 ? B 20 ? 19 1 1 A A 2 1_555 B DT 9 1_555 -0.188 -0.286 -0.102 -9.731 -14.305 6.859 2 A_A2:DT19_B A 2 ? B 19 ? 20 1 1 A A 3 1_555 B DT 8 1_555 -0.135 -0.336 0.195 -2.644 -11.049 2.428 3 A_A3:DT18_B A 3 ? B 18 ? 20 1 1 A G 4 1_555 B DC 7 1_555 -0.286 -0.342 -0.076 -4.889 -8.075 0.092 4 A_G4:DC17_B A 4 ? B 17 ? 19 1 1 A A 5 1_555 B DT 6 1_555 0.120 -0.323 -0.537 -15.062 -7.754 -1.655 5 A_A5:DT16_B A 5 ? B 16 ? 20 1 1 A G 6 1_555 B DC 5 1_555 -0.183 -0.203 -0.289 -9.736 -3.786 -4.224 6 A_G6:DC15_B A 6 ? B 15 ? 19 1 1 A A 7 1_555 B DT 4 1_555 0.097 -0.185 -0.335 -16.711 -5.853 0.799 7 A_A7:DT14_B A 7 ? B 14 ? 20 1 1 A A 8 1_555 B DT 3 1_555 0.066 -0.128 0.175 -1.682 -2.850 -2.013 8 A_A8:DT13_B A 8 ? B 13 ? 20 1 1 A G 9 1_555 B DC 2 1_555 -0.128 -0.248 0.019 -3.240 -6.405 -1.034 9 A_G9:DC12_B A 9 ? B 12 ? 19 1 1 A C 10 1_555 B DG 1 1_555 0.209 -0.163 -0.013 4.807 1.705 0.755 10 A_C10:DG11_B A 10 ? B 11 ? 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 G 1 1_555 B DC 10 1_555 A A 2 1_555 B DT 9 1_555 0.240 -0.996 3.266 -0.365 8.226 32.707 -3.007 -0.470 2.934 14.326 0.636 33.700 1 AA_G1A2:DT19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A A 2 1_555 B DT 9 1_555 A A 3 1_555 B DT 8 1_555 0.109 -0.803 3.087 -1.819 3.033 32.954 -1.884 -0.476 2.994 5.327 3.196 33.138 2 AA_A2A3:DT18DT19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A A 3 1_555 B DT 8 1_555 A G 4 1_555 B DC 7 1_555 0.493 -2.134 3.416 2.544 3.923 27.325 -5.408 -0.411 3.117 8.229 -5.336 27.715 3 AA_A3G4:DC17DT18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A G 4 1_555 B DC 7 1_555 A A 5 1_555 B DT 6 1_555 -1.238 -1.701 3.572 0.353 10.197 33.414 -4.408 2.118 2.930 17.241 -0.596 34.894 4 AA_G4A5:DT16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A A 5 1_555 B DT 6 1_555 A G 6 1_555 B DC 5 1_555 0.992 -1.821 3.319 1.391 8.102 25.020 -6.038 -1.829 2.658 18.089 -3.106 26.315 5 AA_A5G6:DC15DT16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A G 6 1_555 B DC 5 1_555 A A 7 1_555 B DT 4 1_555 0.487 -1.917 3.742 4.676 8.924 30.950 -5.106 0.011 3.122 16.193 -8.485 32.510 6 AA_G6A7:DT14DC15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A A 7 1_555 B DT 4 1_555 A A 8 1_555 B DT 3 1_555 1.013 -1.862 3.031 -0.049 1.973 24.739 -4.870 -2.371 2.874 4.596 0.115 24.817 7 AA_A7A8:DT13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A A 8 1_555 B DT 3 1_555 A G 9 1_555 B DC 2 1_555 -0.414 -1.926 3.472 0.154 1.429 28.993 -4.171 0.861 3.373 2.852 -0.307 29.028 8 AA_A8G9:DC12DT13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A G 9 1_555 B DC 2 1_555 A C 10 1_555 B DG 1 1_555 0.326 -1.509 3.190 -0.686 3.281 32.812 -3.189 -0.686 3.022 5.789 1.211 32.978 9 AA_G9C10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 404D _atom_sites.fract_transf_matrix[1][1] 0.038880 _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] 0.021954 _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] 0.020916 _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_