data_3LTU # _entry.id 3LTU # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 3LTU pdb_00003ltu 10.2210/pdb3ltu/pdb NDB NA0452 ? ? RCSB RCSB057722 ? ? WWPDB D_1000057722 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1DNS . unspecified PDB 3IJK . unspecified PDB 3LTR . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3LTU _pdbx_database_status.recvd_initial_deposition_date 2010-02-16 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sheng, J.' 1 'Hassan, A.E.A.' 2 'Zhang, W.' 3 'Gan, J.' 4 'Huang, Z.' 5 # _citation.id primary _citation.title 'Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate' _citation.journal_abbrev Chemistryselect _citation.journal_volume 8 _citation.page_first ? _citation.page_last ? _citation.year 2023 _citation.journal_id_ASTM ? _citation.country DE _citation.journal_id_ISSN 2365-6549 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI 10.1002/slct.202302253 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Fang, Z.' 1 ? primary 'Dantsu, Y.' 2 ? primary 'Chen, C.' 3 ? primary 'Zhang, W.' 4 ? primary 'Huang, Z.' 5 ? # _cell.entry_id 3LTU _cell.length_a 43.078 _cell.length_b 43.078 _cell.length_c 23.814 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3LTU _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*GP*(UMS)P*GP*(T5S)P*AP*CP*AP*C)-3'" 2584.537 1 ? ? ? ? 2 water nat water 18.015 38 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(UMS)(DG)(T5S)(DA)(DC)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GUGTACAC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # 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 UMS n 1 3 DG n 1 4 T5S n 1 5 DA n 1 6 DC n 1 7 DA n 1 8 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'synthesized by solid phase synthesizer.' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3LTU _struct_ref.pdbx_db_accession 3LTU _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GUGTACAC _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3LTU _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3LTU _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 8 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 T5S 'DNA linking' n ;2'-deoxy-5-(methylselanyl)uridine 5'-phosphate ; ? 'C10 H15 N2 O8 P Se' 401.168 UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ? 'C10 H15 N2 O8 P Se' 401.168 # _exptl.entry_id 3LTU _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.14 _exptl_crystal.density_percent_sol 42.45 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;10% v / v MPD, 40 mM Na Cacodylate pH 6.0, 12 mM Spermine tetra-HCl, 80 mM Sodium Chloride, 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 99 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2009-10-10 _diffrn_detector.details Mirror # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(III)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X12C' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X12C _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 3LTU _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.40 _reflns.number_obs 4661 _reflns.number_all 4766 _reflns.percent_possible_obs 97.8 _reflns.pdbx_Rmerge_I_obs 0.087 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 18.9 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 23 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.40 _reflns_shell.d_res_low 1.45 _reflns_shell.percent_possible_all 99.3 _reflns_shell.Rmerge_I_obs 0.136 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 14.5 _reflns_shell.pdbx_redundancy 11.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 446 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3LTU _refine.ls_number_reflns_obs 4421 _refine.ls_number_reflns_all 4519 _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 30.46 _refine.ls_d_res_high 1.40 _refine.ls_percent_reflns_obs 97.83 _refine.ls_R_factor_obs 0.17584 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.17477 _refine.ls_R_factor_R_free 0.20041 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 212 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.946 _refine.correlation_coeff_Fo_to_Fc_free 0.945 _refine.B_iso_mean 8.965 _refine.aniso_B[1][1] 0.17 _refine.aniso_B[2][2] 0.17 _refine.aniso_B[3][3] -0.34 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 1DNS _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.059 _refine.pdbx_overall_ESU_R_Free 0.061 _refine.overall_SU_ML 0.030 _refine.overall_SU_B 1.465 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3LTU _refine_analyze.Luzzati_coordinate_error_obs 0.059 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.061 _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 163 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 201 _refine_hist.d_res_high 1.40 _refine_hist.d_res_low 30.46 # 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 r_bond_refined_d 0.004 0.021 ? 182 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.108 3.000 ? 278 'X-RAY DIFFRACTION' ? r_chiral_restr 0.044 0.200 ? 32 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 83 'X-RAY DIFFRACTION' ? r_nbd_refined 0.129 0.200 ? 60 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.271 0.200 ? 107 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.098 0.200 ? 24 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.180 0.200 ? 22 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.070 0.200 ? 14 'X-RAY DIFFRACTION' ? r_scbond_it 0.735 3.000 ? 263 'X-RAY DIFFRACTION' ? r_scangle_it 0.976 4.500 ? 278 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.400 _refine_ls_shell.d_res_low 1.436 _refine_ls_shell.number_reflns_R_work 321 _refine_ls_shell.R_factor_R_work 0.161 _refine_ls_shell.percent_reflns_obs 99.40 _refine_ls_shell.R_factor_R_free 0.189 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 12 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3LTU _struct.title '5-SeMe-dU containing DNA 8mer' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3LTU _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, oligonucleotide, 5-SeMe, selenium, 5-methoxy-uridine' # 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_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 1 "O3'" ? ? ? 1_555 A UMS 2 P ? ? A DG 1 A UMS 2 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale both ? A UMS 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A UMS 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale3 covale both ? A DG 3 "O3'" ? ? ? 1_555 A T5S 4 P ? ? A DG 3 A T5S 4 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? A T5S 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? A T5S 4 A DA 5 1_555 ? ? ? ? ? ? ? 1.598 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 1 A DC 8 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 1 A DC 8 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 1 A DC 8 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A UMS 2 N3 ? ? ? 1_555 A DA 7 N1 ? ? A UMS 2 A DA 7 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A UMS 2 O4 ? ? ? 1_555 A DA 7 N6 ? ? A UMS 2 A DA 7 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 6 N3 ? ? A DG 3 A DC 6 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 3 A DC 6 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 6 N4 ? ? A DG 3 A DC 6 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A T5S 4 N3 ? ? ? 1_555 A DA 5 N1 ? ? A T5S 4 A DA 5 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A T5S 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A T5S 4 A DA 5 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A T5S 4 N3 ? ? A DA 5 A T5S 4 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A T5S 4 O4 ? ? A DA 5 A T5S 4 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 A UMS 2 N3 ? ? A DA 7 A UMS 2 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 A UMS 2 O4 ? ? A DA 7 A UMS 2 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 8 A DG 1 8_666 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 3LTU _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 # _atom_sites.entry_id 3LTU _atom_sites.fract_transf_matrix[1][1] 0.023214 _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] 0.023214 _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] 0.041992 _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 SE # 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 UMS 2 2 2 UMS UMS A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 T5S 4 4 4 T5S T5S A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . 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 B 2 HOH 1 9 9 HOH HOH A . B 2 HOH 2 10 10 HOH HOH A . B 2 HOH 3 11 11 HOH HOH A . B 2 HOH 4 12 12 HOH HOH A . B 2 HOH 5 13 13 HOH HOH A . B 2 HOH 6 14 14 HOH HOH A . B 2 HOH 7 15 15 HOH HOH A . B 2 HOH 8 16 16 HOH HOH A . B 2 HOH 9 17 17 HOH HOH A . B 2 HOH 10 18 18 HOH HOH A . B 2 HOH 11 19 19 HOH HOH A . B 2 HOH 12 20 20 HOH HOH A . B 2 HOH 13 21 21 HOH HOH A . B 2 HOH 14 22 22 HOH HOH A . B 2 HOH 15 23 23 HOH HOH A . B 2 HOH 16 24 24 HOH HOH A . B 2 HOH 17 25 25 HOH HOH A . B 2 HOH 18 26 26 HOH HOH A . B 2 HOH 19 27 27 HOH HOH A . B 2 HOH 20 28 28 HOH HOH A . B 2 HOH 21 29 29 HOH HOH A . B 2 HOH 22 30 30 HOH HOH A . B 2 HOH 23 31 31 HOH HOH A . B 2 HOH 24 32 32 HOH HOH A . B 2 HOH 25 33 33 HOH HOH A . B 2 HOH 26 34 34 HOH HOH A . B 2 HOH 27 35 35 HOH HOH A . B 2 HOH 28 36 36 HOH HOH A . B 2 HOH 29 37 37 HOH HOH A . B 2 HOH 30 38 38 HOH HOH A . B 2 HOH 31 39 1 HOH HOH A . B 2 HOH 32 40 2 HOH HOH A . B 2 HOH 33 41 3 HOH HOH A . B 2 HOH 34 42 4 HOH HOH A . B 2 HOH 35 43 5 HOH HOH A . B 2 HOH 36 44 6 HOH HOH A . B 2 HOH 37 45 7 HOH HOH A . B 2 HOH 38 46 8 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A UMS 2 A UMS 2 ? DU ? 2 A T5S 4 A T5S 4 ? DT ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1930 ? 1 MORE 8 ? 1 'SSA (A^2)' 2950 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 8_666 -y+1,-x+1,-z+3/2 0.0000000000 -1.0000000000 0.0000000000 43.0780000000 -1.0000000000 0.0000000000 0.0000000000 43.0780000000 0.0000000000 0.0000000000 -1.0000000000 35.7210000000 # 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 2010-03-09 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-06-13 4 'Structure model' 1 3 2012-09-26 5 'Structure model' 1 4 2023-08-02 6 'Structure model' 1 5 2023-09-06 # _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' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Database references' 4 4 'Structure model' 'Database references' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Source and taxonomy' 8 6 'Structure model' 'Data collection' 9 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' citation 2 5 'Structure model' citation_author 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_entity_src_syn 5 5 'Structure model' struct_conn 6 6 'Structure model' chem_comp_atom 7 6 'Structure model' chem_comp_bond 8 6 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_citation.country' 2 5 'Structure model' '_citation.journal_abbrev' 3 5 'Structure model' '_citation.journal_id_ASTM' 4 5 'Structure model' '_citation.journal_id_CSD' 5 5 'Structure model' '_citation.journal_id_ISSN' 6 5 'Structure model' '_citation.journal_volume' 7 5 'Structure model' '_citation.page_first' 8 5 'Structure model' '_citation.page_last' 9 5 'Structure model' '_citation.pdbx_database_id_DOI' 10 5 'Structure model' '_citation.pdbx_database_id_PubMed' 11 5 'Structure model' '_citation.title' 12 5 'Structure model' '_citation.year' 13 5 'Structure model' '_database_2.pdbx_DOI' 14 5 'Structure model' '_database_2.pdbx_database_accession' 15 5 'Structure model' '_pdbx_entity_src_syn.ncbi_taxonomy_id' 16 5 'Structure model' '_pdbx_entity_src_syn.organism_scientific' 17 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 33.9031 20.2126 16.8362 0.0719 0.0380 0.0470 0.0147 0.0055 -0.0006 0.1441 6.3663 0.0406 -0.1149 0.0753 -0.1495 -0.0140 0.0183 0.0258 -0.3213 0.0111 0.0113 -0.0236 0.0188 0.0030 'X-RAY DIFFRACTION' 2 ? refined 29.2432 4.6948 14.0775 0.0450 0.0206 0.0344 0.0050 -0.0106 -0.0028 3.4846 4.0041 1.9687 2.5919 -0.8465 -1.0934 -0.0736 -0.0286 -0.0367 -0.1712 0.0940 0.0264 0.1441 0.0326 -0.0204 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 1 ? ? A 4 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 5 ? ? A 8 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 PHASES phasing . ? 2 REFMAC refinement 5.2.0019 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # 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 HOH O O N N 108 HOH H1 H N N 109 HOH H2 H N N 110 T5S OP3 O N N 111 T5S P P N N 112 T5S OP1 O N N 113 T5S OP2 O N N 114 T5S "O5'" O N N 115 T5S N1 N N N 116 T5S C6 C N N 117 T5S C2 C N N 118 T5S O2 O N N 119 T5S N3 N N N 120 T5S C4 C N N 121 T5S O4 O N N 122 T5S C5 C N N 123 T5S SE SE N N 124 T5S CH3 C N N 125 T5S "C2'" C N N 126 T5S "C5'" C N N 127 T5S "C4'" C N R 128 T5S "O4'" O N N 129 T5S "C1'" C N R 130 T5S "C3'" C N S 131 T5S "O3'" O N N 132 T5S HOP3 H N N 133 T5S HOP2 H N N 134 T5S H6 H N N 135 T5S HN3 H N N 136 T5S HH3 H N N 137 T5S HH3A H N N 138 T5S HH3B H N N 139 T5S "H2'" H N N 140 T5S "H2'A" H N N 141 T5S "H5'" H N N 142 T5S "H5'A" H N N 143 T5S "H4'" H N N 144 T5S "H1'" H N N 145 T5S "H3'" H N N 146 T5S "HO3'" H N N 147 UMS OP3 O N N 148 UMS P P N N 149 UMS OP1 O N N 150 UMS OP2 O N N 151 UMS "O5'" O N N 152 UMS "C5'" C N N 153 UMS "C4'" C N R 154 UMS "O4'" O N N 155 UMS "C3'" C N R 156 UMS "O3'" O N N 157 UMS "C2'" C N R 158 UMS "SE2'" SE N N 159 UMS "C1'" C N R 160 UMS "CA'" C N N 161 UMS N1 N N N 162 UMS C2 C N N 163 UMS O2 O N N 164 UMS N3 N N N 165 UMS C4 C N N 166 UMS O4 O N N 167 UMS C5 C N N 168 UMS C6 C N N 169 UMS HOP3 H N N 170 UMS HOP2 H N N 171 UMS "H5'" H N N 172 UMS "H5'2" H N N 173 UMS "H4'" H N N 174 UMS "H3'" H N N 175 UMS "HO3'" H N N 176 UMS "H2'" H N N 177 UMS "H1'" H N N 178 UMS "HA'" H N N 179 UMS "HA'2" H N N 180 UMS "HA'3" H N N 181 UMS H3 H N N 182 UMS H5 H N N 183 UMS H6 H N N 184 # 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 HOH O H1 sing N N 113 HOH O H2 sing N N 114 T5S P OP3 sing N N 115 T5S OP3 HOP3 sing N N 116 T5S OP1 P doub N N 117 T5S P OP2 sing N N 118 T5S P "O5'" sing N N 119 T5S OP2 HOP2 sing N N 120 T5S "C5'" "O5'" sing N N 121 T5S "C1'" N1 sing N N 122 T5S C6 N1 sing N N 123 T5S N1 C2 sing N N 124 T5S C6 C5 doub N N 125 T5S C6 H6 sing N N 126 T5S C2 O2 doub N N 127 T5S C2 N3 sing N N 128 T5S C4 N3 sing N N 129 T5S N3 HN3 sing N N 130 T5S C5 C4 sing N N 131 T5S C4 O4 doub N N 132 T5S SE C5 sing N N 133 T5S CH3 SE sing N N 134 T5S CH3 HH3 sing N N 135 T5S CH3 HH3A sing N N 136 T5S CH3 HH3B sing N N 137 T5S "C3'" "C2'" sing N N 138 T5S "C2'" "C1'" sing N N 139 T5S "C2'" "H2'" sing N N 140 T5S "C2'" "H2'A" sing N N 141 T5S "C5'" "C4'" sing N N 142 T5S "C5'" "H5'" sing N N 143 T5S "C5'" "H5'A" sing N N 144 T5S "C3'" "C4'" sing N N 145 T5S "C4'" "O4'" sing N N 146 T5S "C4'" "H4'" sing N N 147 T5S "O4'" "C1'" sing N N 148 T5S "C1'" "H1'" sing N N 149 T5S "O3'" "C3'" sing N N 150 T5S "C3'" "H3'" sing N N 151 T5S "O3'" "HO3'" sing N N 152 UMS OP3 P sing N N 153 UMS OP3 HOP3 sing N N 154 UMS P OP1 doub N N 155 UMS P OP2 sing N N 156 UMS P "O5'" sing N N 157 UMS OP2 HOP2 sing N N 158 UMS "O5'" "C5'" sing N N 159 UMS "C5'" "C4'" sing N N 160 UMS "C5'" "H5'" sing N N 161 UMS "C5'" "H5'2" sing N N 162 UMS "C4'" "O4'" sing N N 163 UMS "C4'" "C3'" sing N N 164 UMS "C4'" "H4'" sing N N 165 UMS "O4'" "C1'" sing N N 166 UMS "C3'" "O3'" sing N N 167 UMS "C3'" "C2'" sing N N 168 UMS "C3'" "H3'" sing N N 169 UMS "O3'" "HO3'" sing N N 170 UMS "C2'" "SE2'" sing N N 171 UMS "C2'" "C1'" sing N N 172 UMS "C2'" "H2'" sing N N 173 UMS "SE2'" "CA'" sing N N 174 UMS "C1'" N1 sing N N 175 UMS "C1'" "H1'" sing N N 176 UMS "CA'" "HA'" sing N N 177 UMS "CA'" "HA'2" sing N N 178 UMS "CA'" "HA'3" sing N N 179 UMS N1 C2 sing N N 180 UMS N1 C6 sing N N 181 UMS C2 O2 doub N N 182 UMS C2 N3 sing N N 183 UMS N3 C4 sing N N 184 UMS N3 H3 sing N N 185 UMS C4 O4 doub N N 186 UMS C4 C5 sing N N 187 UMS C5 C6 doub N N 188 UMS C5 H5 sing N N 189 UMS C6 H6 sing N N 190 # _ndb_struct_conf_na.entry_id 3LTU _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 DG 1 1_555 A DC 8 8_666 -0.343 -0.120 -0.396 -19.126 -13.473 -1.689 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A UMS 2 1_555 A DA 7 8_666 -0.023 -0.082 0.164 -6.710 -10.915 2.899 2 A_UMS2:DA7_A A 2 ? A 7 ? 20 1 1 A DG 3 1_555 A DC 6 8_666 -0.280 -0.188 0.260 -4.428 -12.903 0.261 3 A_DG3:DC6_A A 3 ? A 6 ? 19 1 1 A T5S 4 1_555 A DA 5 8_666 -0.171 -0.153 0.479 -7.992 -9.242 -4.272 4 A_T5S4:DA5_A A 4 ? A 5 ? 20 1 1 A DA 5 1_555 A T5S 4 8_666 0.171 -0.153 0.479 7.992 -9.242 -4.272 5 A_DA5:T5S4_A A 5 ? A 4 ? 20 1 1 A DC 6 1_555 A DG 3 8_666 0.280 -0.188 0.260 4.428 -12.902 0.261 6 A_DC6:DG3_A A 6 ? A 3 ? 19 1 1 A DA 7 1_555 A UMS 2 8_666 0.023 -0.082 0.164 6.710 -10.915 2.899 7 A_DA7:UMS2_A A 7 ? A 2 ? 20 1 1 A DC 8 1_555 A DG 1 8_666 0.343 -0.120 -0.396 19.126 -13.473 -1.689 8 A_DC8:DG1_A A 8 ? A 1 ? 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 A DC 8 8_666 A UMS 2 1_555 A DA 7 8_666 0.512 -0.807 3.092 -3.398 13.604 30.830 -3.348 -1.371 2.460 24.088 6.016 33.799 1 AA_DG1UMS2:DA7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A UMS 2 1_555 A DA 7 8_666 A DG 3 1_555 A DC 6 8_666 0.734 -1.521 3.027 0.106 12.227 28.424 -4.836 -1.361 2.204 23.569 -0.204 30.893 2 AA_UMS2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DG 3 1_555 A DC 6 8_666 A T5S 4 1_555 A DA 5 8_666 -0.343 -1.925 3.350 -0.901 -0.096 35.893 -3.108 0.424 3.362 -0.157 1.462 35.904 3 AA_DG3T5S4:DA5DC6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A T5S 4 1_555 A DA 5 8_666 A DA 5 1_555 A T5S 4 8_666 0.000 -1.615 2.781 0.000 1.563 28.610 -3.558 0.000 2.691 3.160 0.000 28.652 4 AA_T5S4DA5:T5S4DA5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DA 5 1_555 A T5S 4 8_666 A DC 6 1_555 A DG 3 8_666 0.343 -1.925 3.350 0.901 -0.097 35.893 -3.108 -0.424 3.362 -0.157 -1.462 35.904 5 AA_DA5DC6:DG3T5S4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A DC 6 1_555 A DG 3 8_666 A DA 7 1_555 A UMS 2 8_666 -0.734 -1.521 3.027 -0.106 12.227 28.424 -4.836 1.361 2.204 23.569 0.204 30.893 6 AA_DC6DA7:UMS2DG3_AA A 6 ? A 3 ? A 7 ? A 2 ? 1 A DA 7 1_555 A UMS 2 8_666 A DC 8 1_555 A DG 1 8_666 -0.512 -0.807 3.092 3.398 13.604 30.830 -3.348 1.371 2.460 24.088 -6.017 33.798 7 AA_DA7DC8:DG1UMS2_AA A 7 ? A 2 ? A 8 ? A 1 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1DNS _pdbx_initial_refinement_model.details ? #