data_3AJK # _entry.id 3AJK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 3AJK pdb_00003ajk 10.2210/pdb3ajk/pdb NDB NA0578 ? ? RCSB RCSB029330 ? ? WWPDB D_1000029330 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3AJJ 'The same DNA without drug.' unspecified PDB 3AJL 'The same DNA with DAPI' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3AJK _pdbx_database_status.recvd_initial_deposition_date 2010-06-07 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 'Tsunoda, M.' 1 'Sakaue, T.' 2 'Ueno, Y.' 3 'Matsuda, A.' 4 'Takenaka, A.' 5 # _citation.id primary _citation.title 'Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil' _citation.journal_abbrev 'J Nucleic Acids' _citation.journal_volume 2010 _citation.page_first 107289 _citation.page_last 107289 _citation.year 2010 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 2090-0201 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20976303 _citation.pdbx_database_id_DOI 10.4061/2010/107289 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Tsunoda, M.' 1 ? primary 'Sakaue, T.' 2 ? primary 'Naito, S.' 3 ? primary 'Sunami, T.' 4 ? primary 'Abe, N.' 5 ? primary 'Ueno, Y.' 6 ? primary 'Matsuda, A.' 7 ? primary 'Takenaka, A.' 8 ? # _cell.entry_id 3AJK _cell.length_a 25.327 _cell.length_b 40.331 _cell.length_c 65.961 _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 3AJK _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # 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(*CP*GP*CP*GP*GP*AP*TP*(UFR)P*CP*GP*CP*G*)-3'" 3693.375 2 ? ? ? ? 2 non-polymer syn "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" 424.498 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 123 ? ? ? ? # _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 '(DC)(DG)(DC)(DG)(DG)(DA)(DT)(UFR)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGGATUCGCG _entity_poly.pdbx_strand_id A,B _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 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DG n 1 6 DA n 1 7 DT n 1 8 UFR n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Synthetic DNA' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3AJK _struct_ref.pdbx_db_accession 3AJK _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 3AJK A 1 ? 12 ? 3AJK 1 ? 12 ? 1 12 2 1 3AJK B 1 ? 12 ? 3AJK 13 ? 24 ? 13 24 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 HT non-polymer . "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" 'HOECHST 33258' 'C25 H24 N6 O' 424.498 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 UFR 'DNA linking' n ;2'-DEOXY-5-FORMYLURIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C10 H13 N2 O9 P' 336.192 # _exptl.entry_id 3AJK _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.28 _exptl_crystal.density_percent_sol 46.06 _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 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;20mM Na cacodylate, 0.5mM Spermine, 40mM NaCl, 10mM MgCl2, 5% MPD, 0.5mM Hoechst33258, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2001-05-12 _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 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-18B' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-18B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 3AJK _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 34.5 _reflns.d_resolution_high 1.95 _reflns.number_obs 5312 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.042 _reflns.pdbx_Rsym_value 0.040 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_netI_over_sigmaI ? _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.95 _reflns_shell.d_res_low 2.06 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.331 _reflns_shell.pdbx_Rsym_value 0.306 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3AJK _refine.ls_number_reflns_obs 4716 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 1.95 _refine.ls_percent_reflns_obs 99.83 _refine.ls_R_factor_obs 0.20866 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20254 _refine.ls_R_factor_R_free 0.26103 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.8 _refine.ls_number_reflns_R_free 513 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.966 _refine.correlation_coeff_Fo_to_Fc_free 0.949 _refine.B_iso_mean 34.746 _refine.aniso_B[1][1] 2.42 _refine.aniso_B[2][2] -0.77 _refine.aniso_B[3][3] -1.65 _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 1.40 _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 'PDB ENTRY 355D' _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_Free 0.195 _refine.overall_SU_ML 0.133 _refine.overall_SU_B 4.704 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 490 _refine_hist.pdbx_number_atoms_ligand 33 _refine_hist.number_atoms_solvent 123 _refine_hist.number_atoms_total 646 _refine_hist.d_res_high 1.95 _refine_hist.d_res_low 10.00 # 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 0.019 0.021 ? 587 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.096 3.000 ? 898 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.136 0.200 ? 96 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.017 0.020 ? 284 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.956 3.000 ? 587 'X-RAY DIFFRACTION' ? r_scangle_it 4.065 4.500 ? 898 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.950 _refine_ls_shell.d_res_low 1.999 _refine_ls_shell.number_reflns_R_work 325 _refine_ls_shell.R_factor_R_work 0.299 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.405 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 34 _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 3AJK _struct.title 'Crystal structure of d(CGCGGATf5UCGCG): 5-Formyluridine:Guanosine Base-pair in B-DNA with Hoechst33258' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3AJK _struct_keywords.pdbx_keywords DNA _struct_keywords.text '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 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # 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 DT 7 "O3'" ? ? ? 1_555 A UFR 8 P ? ? A DT 7 A UFR 8 1_555 ? ? ? ? ? ? ? 1.563 ? ? covale2 covale both ? B DT 7 "O3'" ? ? ? 1_555 B UFR 8 P ? ? B DT 19 B UFR 20 1_555 ? ? ? ? ? ? ? 1.633 ? ? metalc1 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 1003 1_555 ? ? ? ? ? ? ? 1.912 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 1009 1_555 ? ? ? ? ? ? ? 2.068 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 1010 1_555 ? ? ? ? ? ? ? 1.956 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 1016 1_555 ? ? ? ? ? ? ? 2.203 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 1050 1_555 ? ? ? ? ? ? ? 2.089 ? ? metalc6 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 1060 1_555 ? ? ? ? ? ? ? 2.000 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B UFR 8 O2 ? ? A DG 5 B UFR 20 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B UFR 8 N3 ? ? A DG 5 B UFR 20 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A UFR 8 O4 ? ? ? 1_555 B DG 5 N1 ? ? A UFR 8 B DG 17 1_555 ? ? ? ? ? ? 'UFR-DG MISPAIR' ? ? ? hydrog20 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A HT 25 ? 12 'BINDING SITE FOR RESIDUE HT A 25' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 12 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 12 DT A 7 ? DT A 7 . ? 1_555 ? 3 AC1 12 UFR A 8 ? UFR A 8 . ? 1_555 ? 4 AC1 12 DC A 9 ? DC A 9 . ? 1_555 ? 5 AC1 12 DG A 10 ? DG A 10 . ? 1_555 ? 6 AC1 12 DC A 11 ? DC A 11 . ? 1_555 ? 7 AC1 12 DG B 4 ? DG B 16 . ? 1_555 ? 8 AC1 12 DA B 6 ? DA B 18 . ? 1_555 ? 9 AC1 12 DT B 7 ? DT B 19 . ? 1_555 ? 10 AC1 12 UFR B 8 ? UFR B 20 . ? 1_555 ? 11 AC1 12 DC B 9 ? DC B 21 . ? 1_555 ? 12 AC1 12 DG B 12 ? DG B 24 . ? 2_555 ? # _database_PDB_matrix.entry_id 3AJK _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 3AJK _atom_sites.fract_transf_matrix[1][1] 0.039484 _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] 0.024795 _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] 0.015160 _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 MG N O P # 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 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 UFR 8 8 8 UFR UFR A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 13 13 DC DC B . n B 1 2 DG 2 14 14 DG DG B . n B 1 3 DC 3 15 15 DC DC B . n B 1 4 DG 4 16 16 DG DG B . n B 1 5 DG 5 17 17 DG DG B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 UFR 8 20 20 UFR UFR B . n B 1 9 DC 9 21 21 DC DC B . n B 1 10 DG 10 22 22 DG DG B . n B 1 11 DC 11 23 23 DC DC B . n B 1 12 DG 12 24 24 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HT 1 25 25 HT HT A . D 3 MG 1 101 101 MG MG A . E 4 HOH 1 1001 1001 HOH HOH A . E 4 HOH 2 1002 1002 HOH HOH A . E 4 HOH 3 1003 1003 HOH HOH A . E 4 HOH 4 1004 1004 HOH HOH A . E 4 HOH 5 1006 1006 HOH HOH A . E 4 HOH 6 1007 1007 HOH HOH A . E 4 HOH 7 1008 1008 HOH HOH A . E 4 HOH 8 1009 1009 HOH HOH A . E 4 HOH 9 1010 1010 HOH HOH A . E 4 HOH 10 1012 1012 HOH HOH A . E 4 HOH 11 1013 1013 HOH HOH A . E 4 HOH 12 1015 1015 HOH HOH A . E 4 HOH 13 1016 1016 HOH HOH A . E 4 HOH 14 1019 1019 HOH HOH A . E 4 HOH 15 1020 1020 HOH HOH A . E 4 HOH 16 1021 1021 HOH HOH A . E 4 HOH 17 1023 1023 HOH HOH A . E 4 HOH 18 1024 1024 HOH HOH A . E 4 HOH 19 1025 1025 HOH HOH A . E 4 HOH 20 1028 1028 HOH HOH A . E 4 HOH 21 1029 1029 HOH HOH A . E 4 HOH 22 1031 1031 HOH HOH A . E 4 HOH 23 1032 1032 HOH HOH A . E 4 HOH 24 1034 1034 HOH HOH A . E 4 HOH 25 1035 1035 HOH HOH A . E 4 HOH 26 1037 1037 HOH HOH A . E 4 HOH 27 1039 1039 HOH HOH A . E 4 HOH 28 1040 1040 HOH HOH A . E 4 HOH 29 1042 1042 HOH HOH A . E 4 HOH 30 1045 1045 HOH HOH A . E 4 HOH 31 1048 1048 HOH HOH A . E 4 HOH 32 1050 1050 HOH HOH A . E 4 HOH 33 1052 1052 HOH HOH A . E 4 HOH 34 1053 1053 HOH HOH A . E 4 HOH 35 1054 1054 HOH HOH A . E 4 HOH 36 1056 1056 HOH HOH A . E 4 HOH 37 1057 1057 HOH HOH A . E 4 HOH 38 1058 1058 HOH HOH A . E 4 HOH 39 1060 1060 HOH HOH A . E 4 HOH 40 1061 1061 HOH HOH A . E 4 HOH 41 1063 1063 HOH HOH A . E 4 HOH 42 1066 1066 HOH HOH A . E 4 HOH 43 1069 1069 HOH HOH A . E 4 HOH 44 1070 1070 HOH HOH A . E 4 HOH 45 1072 1072 HOH HOH A . E 4 HOH 46 1074 1074 HOH HOH A . E 4 HOH 47 1075 1075 HOH HOH A . E 4 HOH 48 1076 1076 HOH HOH A . E 4 HOH 49 1077 1077 HOH HOH A . E 4 HOH 50 1079 1079 HOH HOH A . E 4 HOH 51 1080 1080 HOH HOH A . E 4 HOH 52 1081 1081 HOH HOH A . E 4 HOH 53 1082 1082 HOH HOH A . E 4 HOH 54 1086 1086 HOH HOH A . E 4 HOH 55 1087 1087 HOH HOH A . E 4 HOH 56 1088 1088 HOH HOH A . E 4 HOH 57 1089 1089 HOH HOH A . E 4 HOH 58 1090 1090 HOH HOH A . E 4 HOH 59 1093 1093 HOH HOH A . E 4 HOH 60 1094 1094 HOH HOH A . E 4 HOH 61 1096 1096 HOH HOH A . E 4 HOH 62 1098 1098 HOH HOH A . E 4 HOH 63 1099 1099 HOH HOH A . E 4 HOH 64 1100 1100 HOH HOH A . E 4 HOH 65 1101 1101 HOH HOH A . E 4 HOH 66 1102 1102 HOH HOH A . E 4 HOH 67 1104 1104 HOH HOH A . E 4 HOH 68 1106 1106 HOH HOH A . E 4 HOH 69 1107 1107 HOH HOH A . E 4 HOH 70 1109 1109 HOH HOH A . E 4 HOH 71 1110 1110 HOH HOH A . E 4 HOH 72 1111 1111 HOH HOH A . E 4 HOH 73 1114 1114 HOH HOH A . E 4 HOH 74 1115 1115 HOH HOH A . E 4 HOH 75 1116 1116 HOH HOH A . E 4 HOH 76 1118 1118 HOH HOH A . E 4 HOH 77 1119 1119 HOH HOH A . E 4 HOH 78 1120 1120 HOH HOH A . E 4 HOH 79 1121 1121 HOH HOH A . E 4 HOH 80 1123 1123 HOH HOH A . E 4 HOH 81 1124 1124 HOH HOH A . F 4 HOH 1 1005 1005 HOH HOH B . F 4 HOH 2 1011 1011 HOH HOH B . F 4 HOH 3 1014 1014 HOH HOH B . F 4 HOH 4 1017 1017 HOH HOH B . F 4 HOH 5 1018 1018 HOH HOH B . F 4 HOH 6 1022 1022 HOH HOH B . F 4 HOH 7 1026 1026 HOH HOH B . F 4 HOH 8 1027 1027 HOH HOH B . F 4 HOH 9 1030 1030 HOH HOH B . F 4 HOH 10 1036 1036 HOH HOH B . F 4 HOH 11 1038 1038 HOH HOH B . F 4 HOH 12 1041 1041 HOH HOH B . F 4 HOH 13 1043 1043 HOH HOH B . F 4 HOH 14 1044 1044 HOH HOH B . F 4 HOH 15 1046 1046 HOH HOH B . F 4 HOH 16 1047 1047 HOH HOH B . F 4 HOH 17 1049 1049 HOH HOH B . F 4 HOH 18 1051 1051 HOH HOH B . F 4 HOH 19 1055 1055 HOH HOH B . F 4 HOH 20 1059 1059 HOH HOH B . F 4 HOH 21 1062 1062 HOH HOH B . F 4 HOH 22 1064 1064 HOH HOH B . F 4 HOH 23 1065 1065 HOH HOH B . F 4 HOH 24 1067 1067 HOH HOH B . F 4 HOH 25 1068 1068 HOH HOH B . F 4 HOH 26 1071 1071 HOH HOH B . F 4 HOH 27 1073 1073 HOH HOH B . F 4 HOH 28 1078 1078 HOH HOH B . F 4 HOH 29 1083 1083 HOH HOH B . F 4 HOH 30 1084 1084 HOH HOH B . F 4 HOH 31 1085 1085 HOH HOH B . F 4 HOH 32 1091 1091 HOH HOH B . F 4 HOH 33 1092 1092 HOH HOH B . F 4 HOH 34 1095 1095 HOH HOH B . F 4 HOH 35 1097 1097 HOH HOH B . F 4 HOH 36 1103 1103 HOH HOH B . F 4 HOH 37 1105 1105 HOH HOH B . F 4 HOH 38 1108 1108 HOH HOH B . F 4 HOH 39 1112 1112 HOH HOH B . F 4 HOH 40 1113 1113 HOH HOH B . F 4 HOH 41 1117 1117 HOH HOH B . F 4 HOH 42 1122 1122 HOH HOH B . # 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 UFR 8 A UFR 8 ? DU ? 2 B UFR 8 B UFR 20 ? DU ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # _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 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # 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)' 2350 ? 1 MORE 5 ? 1 'SSA (A^2)' 4290 ? # _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_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 1003 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1009 ? 1_555 86.8 ? 2 O ? E HOH . ? A HOH 1003 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1010 ? 1_555 174.3 ? 3 O ? E HOH . ? A HOH 1009 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1010 ? 1_555 89.9 ? 4 O ? E HOH . ? A HOH 1003 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1016 ? 1_555 82.1 ? 5 O ? E HOH . ? A HOH 1009 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1016 ? 1_555 168.9 ? 6 O ? E HOH . ? A HOH 1010 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1016 ? 1_555 101.2 ? 7 O ? E HOH . ? A HOH 1003 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1050 ? 1_555 85.4 ? 8 O ? E HOH . ? A HOH 1009 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1050 ? 1_555 89.1 ? 9 O ? E HOH . ? A HOH 1010 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1050 ? 1_555 90.0 ? 10 O ? E HOH . ? A HOH 1016 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1050 ? 1_555 89.5 ? 11 O ? E HOH . ? A HOH 1003 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1060 ? 1_555 88.3 ? 12 O ? E HOH . ? A HOH 1009 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1060 ? 1_555 83.8 ? 13 O ? E HOH . ? A HOH 1010 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1060 ? 1_555 95.9 ? 14 O ? E HOH . ? A HOH 1016 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1060 ? 1_555 96.4 ? 15 O ? E HOH . ? A HOH 1050 ? 1_555 MG ? D MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 1060 ? 1_555 170.7 ? # 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 2011-04-27 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-11-01 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.value' 6 3 'Structure model' '_struct_conn.pdbx_dist_value' 7 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 9 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 10 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 11 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 AMoRE phasing . ? 2 REFMAC refinement 5.5.0102 ? 3 DPS 'data reduction' . ? 4 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O5 A UFR 8 ? ? O A HOH 1120 ? ? 2.01 2 1 OP2 A DG 12 ? ? O A HOH 1058 ? ? 2.10 # 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 DG 5 ? ? N3 A DG 5 ? ? 1.375 1.323 0.052 0.008 N 2 1 "O4'" A DG 10 ? ? "C4'" A DG 10 ? ? 1.514 1.449 0.065 0.009 N 3 1 "O3'" A DG 10 ? ? "C3'" A DG 10 ? ? 1.369 1.419 -0.050 0.006 N 4 1 "O3'" B DC 13 ? ? "C3'" B DC 13 ? ? 1.349 1.419 -0.070 0.006 N 5 1 "O3'" B DC 15 ? ? "C3'" B DC 15 ? ? 1.375 1.419 -0.044 0.006 N 6 1 N3 B DG 16 ? ? C4 B DG 16 ? ? 1.403 1.350 0.053 0.007 N 7 1 C5 B DG 16 ? ? N7 B DG 16 ? ? 1.437 1.388 0.049 0.006 N 8 1 "O3'" B DT 19 ? ? "C3'" B DT 19 ? ? 1.383 1.419 -0.036 0.006 N 9 1 N1 B DC 21 ? ? C6 B DC 21 ? ? 1.411 1.367 0.044 0.006 N 10 1 "O3'" B DG 22 ? ? "C3'" B DG 22 ? ? 1.348 1.419 -0.071 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A DC 1 ? A "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 103.86 109.40 -5.54 0.80 N 2 1 N3 A DC 1 ? ? C4 A DC 1 ? ? C5 A DC 1 ? ? 119.11 121.90 -2.79 0.40 N 3 1 C2 A DG 2 ? ? N3 A DG 2 ? ? C4 A DG 2 ? ? 115.98 111.90 4.08 0.50 N 4 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 103.67 108.00 -4.33 0.70 N 5 1 N3 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 126.38 121.90 4.48 0.70 N 6 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? "C2'" A DG 4 ? ? 109.81 106.80 3.01 0.50 N 7 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 116.24 108.30 7.94 0.30 N 8 1 "O5'" A DG 5 ? ? "C5'" A DG 5 ? ? "C4'" A DG 5 ? ? 103.05 109.40 -6.35 0.80 N 9 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 103.06 108.00 -4.94 0.70 N 10 1 OP1 A DA 6 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 129.20 119.60 9.60 1.50 N 11 1 "O5'" A DA 6 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 99.96 105.70 -5.74 0.90 N 12 1 "O5'" A DA 6 ? ? "C5'" A DA 6 ? ? "C4'" A DA 6 ? ? 104.00 109.40 -5.40 0.80 N 13 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 101.11 108.00 -6.89 0.70 N 14 1 OP1 A DT 7 ? ? P A DT 7 ? ? OP2 A DT 7 ? ? 128.93 119.60 9.33 1.50 N 15 1 "O5'" A DT 7 ? ? P A DT 7 ? ? OP2 A DT 7 ? ? 95.43 105.70 -10.27 0.90 N 16 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 101.87 108.00 -6.13 0.70 N 17 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 103.80 108.00 -4.20 0.70 N 18 1 N1 A DG 12 ? ? C6 A DG 12 ? ? O6 A DG 12 ? ? 123.72 119.90 3.82 0.60 N 19 1 C5 A DG 12 ? ? C6 A DG 12 ? ? O6 A DG 12 ? ? 123.08 128.60 -5.52 0.60 N 20 1 "C3'" B DC 13 ? ? "C2'" B DC 13 ? ? "C1'" B DC 13 ? ? 95.57 102.40 -6.83 0.80 N 21 1 "O4'" B DC 13 ? ? "C1'" B DC 13 ? ? N1 B DC 13 ? ? 111.02 108.30 2.72 0.30 N 22 1 C6 B DC 13 ? ? N1 B DC 13 ? ? C2 B DC 13 ? ? 122.82 120.30 2.52 0.40 N 23 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 102.31 108.00 -5.69 0.70 N 24 1 N1 B DG 14 ? ? C6 B DG 14 ? ? O6 B DG 14 ? ? 123.50 119.90 3.60 0.60 N 25 1 C5 B DG 14 ? ? C6 B DG 14 ? ? O6 B DG 14 ? ? 123.63 128.60 -4.97 0.60 N 26 1 OP1 B DG 16 ? ? P B DG 16 ? ? OP2 B DG 16 ? ? 128.87 119.60 9.27 1.50 N 27 1 "O4'" B DG 17 ? ? "C1'" B DG 17 ? ? N9 B DG 17 ? ? 111.09 108.30 2.79 0.30 N 28 1 C5 B DG 17 ? ? C6 B DG 17 ? ? O6 B DG 17 ? ? 124.05 128.60 -4.55 0.60 N 29 1 OP1 B DT 19 ? ? P B DT 19 ? ? OP2 B DT 19 ? ? 129.48 119.60 9.88 1.50 N 30 1 "C1'" B DT 19 ? ? "O4'" B DT 19 ? ? "C4'" B DT 19 ? ? 103.16 110.10 -6.94 1.00 N 31 1 "O4'" B DC 21 ? ? "C1'" B DC 21 ? ? N1 B DC 21 ? ? 97.17 108.00 -10.83 0.70 N 32 1 "O4'" B DC 23 ? ? "C1'" B DC 23 ? ? N1 B DC 23 ? ? 101.34 108.00 -6.66 0.70 N 33 1 N3 B DC 23 ? ? C4 B DC 23 ? ? C5 B DC 23 ? ? 124.55 121.90 2.65 0.40 N 34 1 C4 B DC 23 ? ? C5 B DC 23 ? ? C6 B DC 23 ? ? 114.35 117.40 -3.05 0.50 N 35 1 "O5'" B DG 24 ? ? "C5'" B DG 24 ? ? "C4'" B DG 24 ? ? 103.08 109.40 -6.32 0.80 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 HT O1 O N N 147 HT C1 C Y N 148 HT C4 C Y N 149 HT C2 C Y N 150 HT C3 C Y N 151 HT C6 C Y N 152 HT C5 C Y N 153 HT C7 C Y N 154 HT N1 N Y N 155 HT C8 C Y N 156 HT C9 C Y N 157 HT N2 N Y N 158 HT C10 C Y N 159 HT C11 C Y N 160 HT C12 C Y N 161 HT C13 C Y N 162 HT C14 C Y N 163 HT N3 N Y N 164 HT C15 C Y N 165 HT C16 C Y N 166 HT N4 N Y N 167 HT C17 C Y N 168 HT C18 C Y N 169 HT C19 C Y N 170 HT C20 C Y N 171 HT N5 N N N 172 HT C21 C N N 173 HT C22 C N N 174 HT N6 N N N 175 HT C23 C N N 176 HT C24 C N N 177 HT C25 C N N 178 HT HO1 H N N 179 HT H2 H N N 180 HT H3 H N N 181 HT H5 H N N 182 HT H6 H N N 183 HT HN1 H N N 184 HT H10 H N N 185 HT H11 H N N 186 HT H13 H N N 187 HT HN3 H N N 188 HT H17 H N N 189 HT H18 H N N 190 HT H20 H N N 191 HT H211 H N N 192 HT H212 H N N 193 HT H221 H N N 194 HT H222 H N N 195 HT H231 H N N 196 HT H232 H N N 197 HT H241 H N N 198 HT H242 H N N 199 HT H253 H N N 200 HT H252 H N N 201 HT H251 H N N 202 MG MG MG N N 203 UFR O3P O N N 204 UFR P P N N 205 UFR O1P O N N 206 UFR O2P O N N 207 UFR "O5'" O N N 208 UFR "C5'" C N N 209 UFR "C4'" C N R 210 UFR "O4'" O N N 211 UFR "C3'" C N S 212 UFR "O3'" O N N 213 UFR "C2'" C N N 214 UFR "C1'" C N R 215 UFR N1 N N N 216 UFR C2 C N N 217 UFR O2 O N N 218 UFR N3 N N N 219 UFR C4 C N N 220 UFR O4 O N N 221 UFR C5 C N N 222 UFR C6 C N N 223 UFR C7 C N N 224 UFR O5 O N N 225 UFR HO1P H N N 226 UFR HO2P H N N 227 UFR "H5'1" H N N 228 UFR "H5'2" H N N 229 UFR "H4'" H N N 230 UFR "H3'" H N N 231 UFR "HO3'" H N N 232 UFR "H2'1" H N N 233 UFR "H2'2" H N N 234 UFR "H1'" H N N 235 UFR HN3 H N N 236 UFR H6 H N N 237 UFR H7 H N N 238 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 HT O1 C1 sing N N 152 HT O1 HO1 sing N N 153 HT C1 C2 doub Y N 154 HT C1 C6 sing Y N 155 HT C2 C3 sing Y N 156 HT C2 H2 sing N N 157 HT C3 C4 doub Y N 158 HT C3 H3 sing N N 159 HT C4 C5 sing Y N 160 HT C4 C7 sing Y N 161 HT C5 C6 doub Y N 162 HT C5 H5 sing N N 163 HT C6 H6 sing N N 164 HT C7 N1 sing Y N 165 HT C7 N2 doub Y N 166 HT N1 C8 sing Y N 167 HT N1 HN1 sing N N 168 HT C8 C9 doub Y N 169 HT C8 C13 sing Y N 170 HT C9 N2 sing Y N 171 HT C9 C10 sing Y N 172 HT C10 C11 doub Y N 173 HT C10 H10 sing N N 174 HT C11 C12 sing Y N 175 HT C11 H11 sing N N 176 HT C12 C13 doub Y N 177 HT C12 C14 sing Y N 178 HT C13 H13 sing N N 179 HT C14 N3 sing Y N 180 HT C14 N4 doub Y N 181 HT N3 C15 sing Y N 182 HT N3 HN3 sing N N 183 HT C15 C16 doub Y N 184 HT C15 C20 sing Y N 185 HT C16 N4 sing Y N 186 HT C16 C17 sing Y N 187 HT C17 C18 doub Y N 188 HT C17 H17 sing N N 189 HT C18 C19 sing Y N 190 HT C18 H18 sing N N 191 HT C19 C20 doub Y N 192 HT C19 N5 sing N N 193 HT C20 H20 sing N N 194 HT N5 C21 sing N N 195 HT N5 C24 sing N N 196 HT C21 C22 sing N N 197 HT C21 H211 sing N N 198 HT C21 H212 sing N N 199 HT C22 N6 sing N N 200 HT C22 H221 sing N N 201 HT C22 H222 sing N N 202 HT N6 C23 sing N N 203 HT N6 C25 sing N N 204 HT C23 C24 sing N N 205 HT C23 H231 sing N N 206 HT C23 H232 sing N N 207 HT C24 H241 sing N N 208 HT C24 H242 sing N N 209 HT C25 H253 sing N N 210 HT C25 H252 sing N N 211 HT C25 H251 sing N N 212 UFR O3P P doub N N 213 UFR P O1P sing N N 214 UFR P O2P sing N N 215 UFR P "O5'" sing N N 216 UFR O1P HO1P sing N N 217 UFR O2P HO2P sing N N 218 UFR "O5'" "C5'" sing N N 219 UFR "C5'" "C4'" sing N N 220 UFR "C5'" "H5'1" sing N N 221 UFR "C5'" "H5'2" sing N N 222 UFR "C4'" "O4'" sing N N 223 UFR "C4'" "C3'" sing N N 224 UFR "C4'" "H4'" sing N N 225 UFR "O4'" "C1'" sing N N 226 UFR "C3'" "O3'" sing N N 227 UFR "C3'" "C2'" sing N N 228 UFR "C3'" "H3'" sing N N 229 UFR "O3'" "HO3'" sing N N 230 UFR "C2'" "C1'" sing N N 231 UFR "C2'" "H2'1" sing N N 232 UFR "C2'" "H2'2" sing N N 233 UFR "C1'" N1 sing N N 234 UFR "C1'" "H1'" sing N N 235 UFR N1 C2 sing N N 236 UFR N1 C6 sing N N 237 UFR C2 O2 doub N N 238 UFR C2 N3 sing N N 239 UFR N3 C4 sing N N 240 UFR N3 HN3 sing N N 241 UFR C4 O4 doub N N 242 UFR C4 C5 sing N N 243 UFR C5 C6 doub N N 244 UFR C5 C7 sing N N 245 UFR C6 H6 sing N N 246 UFR C7 O5 doub N N 247 UFR C7 H7 sing N N 248 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3AJK 'b-form double helix' 3AJK 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.322 -0.283 0.066 0.862 -13.905 -5.168 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.156 -0.141 0.203 -4.235 -13.668 -1.930 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.311 -0.117 0.014 -4.785 -3.962 -0.002 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.547 -0.274 0.280 10.617 -8.185 -0.467 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DG 5 1_555 B UFR 8 1_555 -2.078 -0.582 0.104 8.679 -14.641 -2.429 5 A_DG5:UFR20_B A 5 ? B 20 ? 28 1 1 A DA 6 1_555 B DT 7 1_555 0.050 -0.205 -0.038 2.567 -20.805 3.777 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 0.064 -0.117 -0.056 -4.531 -21.014 0.977 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A UFR 8 1_555 B DG 5 1_555 -2.242 0.000 -0.081 -10.557 -16.341 -7.519 8 A_UFR8:DG17_B A 8 ? B 17 ? ? ? 1 A DC 9 1_555 B DG 4 1_555 0.590 0.063 -0.092 -5.569 -8.990 3.460 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.176 -0.121 0.123 8.392 -7.085 0.964 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.159 -0.235 0.494 -2.586 -17.377 -1.172 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.031 -0.298 0.086 3.260 -5.636 -5.365 12 A_DG12:DC13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.020 0.260 3.391 -1.006 7.697 35.113 -0.727 -0.118 3.370 12.569 1.643 35.934 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.993 0.761 3.354 2.675 -5.651 41.472 1.665 -1.104 3.282 -7.926 -3.752 41.921 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.377 1.058 3.059 1.182 8.775 22.839 -0.210 1.254 3.214 21.167 -2.852 24.474 3 AA_DC3DG4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DG 5 1_555 B UFR 8 1_555 -0.041 -0.576 3.198 -1.956 6.259 29.865 -2.285 -0.295 3.014 11.963 3.739 30.561 4 AA_DG4DG5:UFR20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DG 5 1_555 B UFR 8 1_555 A DA 6 1_555 B DT 7 1_555 0.078 -0.118 3.379 0.242 2.678 45.539 -0.395 -0.078 3.368 3.456 -0.313 45.614 5 AA_DG5DA6:DT19UFR20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.118 -0.542 3.356 0.491 0.003 32.809 -0.959 0.296 3.354 0.006 -0.869 32.813 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A UFR 8 1_555 B DG 5 1_555 0.296 0.004 3.164 3.538 -1.184 33.399 0.194 0.050 3.175 -2.052 -6.132 33.601 7 AA_DT7UFR8:DG17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A UFR 8 1_555 B DG 5 1_555 A DC 9 1_555 B DG 4 1_555 0.146 0.330 3.387 -0.802 -0.396 40.448 0.523 -0.304 3.380 -0.573 1.159 40.457 8 AA_UFR8DC9:DG16DG17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 -0.037 1.003 3.124 -1.716 8.768 28.592 0.125 -0.284 3.277 17.230 3.372 29.927 9 AA_DC9DG10:DC15DG16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -0.789 0.560 3.608 -5.297 -8.701 41.282 1.747 0.496 3.496 -12.120 7.379 42.467 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 0.511 0.571 3.205 5.615 3.049 37.172 0.490 -0.065 3.279 4.739 -8.729 37.698 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" HT 3 'MAGNESIUM ION' MG 4 water 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 355D _pdbx_initial_refinement_model.details 'PDB ENTRY 355D' #