data_3CE5 # _entry.id 3CE5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 3CE5 pdb_00003ce5 10.2210/pdb3ce5/pdb NDB DD0093 ? ? RCSB RCSB046665 ? ? WWPDB D_1000046665 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1K8P _pdbx_database_related.details 'The same sequence without bound ligand' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3CE5 _pdbx_database_status.recvd_initial_deposition_date 2008-02-28 _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 'Campbell, N.H.' 1 'Parkinson, G.N.' 2 'Reszka, A.P.' 3 'Neidle, S.' 4 # _citation.id primary _citation.title 'Structural basis of DNA quadruplex recognition by an acridine drug.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 130 _citation.page_first 6722 _citation.page_last 6724 _citation.year 2008 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18457389 _citation.pdbx_database_id_DOI 10.1021/ja8016973 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Campbell, N.H.' 1 ? primary 'Parkinson, G.N.' 2 ? primary 'Reszka, A.P.' 3 ? primary 'Neidle, S.' 4 ? # _cell.entry_id 3CE5 _cell.length_a 70.338 _cell.length_b 70.338 _cell.length_c 34.293 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _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 3CE5 _symmetry.space_group_name_H-M 'I 4' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _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 ;DNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3') ; 3773.462 2 ? ? ? ? 2 non-polymer syn 'POTASSIUM ION' 39.098 2 ? ? ? ? 3 non-polymer syn '9-[4-(n,n-dimethylamino)phenylamino]-3,6-bis(3-pyrrolidinopropionamido) acridine' 593.762 1 ? ? ? ? 4 water nat water 18.015 54 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)' _entity_poly.pdbx_seq_one_letter_code_can TAGGGTTAGGGT _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 DT n 1 2 DA n 1 3 DG n 1 4 DG n 1 5 DG n 1 6 DT n 1 7 DT n 1 8 DA n 1 9 DG n 1 10 DG n 1 11 DG n 1 12 DT 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 'This quadruplex-forming sequence occurs naturally in the telomeric ends of human chromosomes' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3CE5 _struct_ref.pdbx_db_accession 3CE5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code TAGGGTTAGGGT _struct_ref.pdbx_align_begin 1 _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 3CE5 A 1 ? 12 ? 3CE5 1 ? 12 ? 1 12 2 1 3CE5 B 1 ? 12 ? 3CE5 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 BRA non-polymer . '9-[4-(n,n-dimethylamino)phenylamino]-3,6-bis(3-pyrrolidinopropionamido) acridine' "N,N'-(9-{[4-(dimethylamino)phenyl]amino}acridine-3,6-diyl)bis(3-pyrrolidin-1-ylpropanamide)" 'C35 H43 N7 O2' 593.762 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 # _exptl.entry_id 3CE5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.81 _exptl_crystal.density_percent_sol 56.23 _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 285.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details ;1.6 mM DNA, 1.6 mM BRACO19, 200 mM ammonium sulphate, 20 mM sodium chloride, 20 mM potassium chloride, 20 mM lithium sulphate and 36 mM potassium cacodylate buffer at pH 6.5 equilibrated against 1.6 M ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 285.15K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 '200 mM ammonium sulphate' ? ? ? 1 2 1 'sodium chloride' ? ? ? 1 3 1 'potassium chloride' ? ? ? 1 4 1 'lithium sulphate' ? ? ? 1 5 1 'potassium cacodylate' ? ? ? 1 6 1 'BRACO19, the ligand under code BRA' ? ? ? 1 7 2 '1.6 M ammonium sulphate' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 105 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2008-01-15 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'osmic mirrors' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3CE5 _reflns.observed_criterion_sigma_F . _reflns.observed_criterion_sigma_I 3.0 _reflns.d_resolution_high 2.50 _reflns.d_resolution_low 35.17 _reflns.number_all 3003 _reflns.number_obs 2994 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.065 _reflns.pdbx_Rsym_value . _reflns.pdbx_netI_over_sigmaI 9.8 _reflns.B_iso_Wilson_estimate 58.2 _reflns.pdbx_redundancy 2.90 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.50 _reflns_shell.d_res_low 2.59 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.310 _reflns_shell.pdbx_Rsym_value . _reflns_shell.meanI_over_sigI_obs 2.4 _reflns_shell.pdbx_redundancy 2.80 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 291 _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 3CE5 _refine.ls_number_reflns_obs 2852 _refine.ls_number_reflns_all 2992 _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 35.17 _refine.ls_d_res_high 2.50 _refine.ls_percent_reflns_obs 100.00 _refine.ls_R_factor_obs 0.18446 _refine.ls_R_factor_all 0.18446 _refine.ls_R_factor_R_work 0.18298 _refine.ls_R_factor_R_free 0.21341 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 140 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.960 _refine.correlation_coeff_Fo_to_Fc_free 0.965 _refine.B_iso_mean 23.482 _refine.aniso_B[1][1] 2.08 _refine.aniso_B[2][2] 2.08 _refine.aniso_B[3][3] -4.15 _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 1K8P' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model isotropic _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 0.550 _refine.pdbx_overall_ESU_R_Free 0.250 _refine.overall_SU_ML 0.160 _refine.overall_SU_B 7.026 _refine.ls_redundancy_reflns_obs ? _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_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 502 _refine_hist.pdbx_number_atoms_ligand 46 _refine_hist.number_atoms_solvent 54 _refine_hist.number_atoms_total 602 _refine_hist.d_res_high 2.50 _refine_hist.d_res_low 35.17 # 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 0.024 0.021 ? 617 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.813 2.994 ? 948 'X-RAY DIFFRACTION' ? r_chiral_restr 0.115 0.200 ? 95 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.016 0.020 ? 307 'X-RAY DIFFRACTION' ? r_nbd_refined 0.306 0.200 ? 186 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.342 0.200 ? 335 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.207 0.200 ? 36 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.162 0.200 ? 2 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.193 0.200 ? 24 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.196 0.200 ? 2 'X-RAY DIFFRACTION' ? r_scbond_it 2.845 3.000 ? 683 'X-RAY DIFFRACTION' ? r_scangle_it 3.864 4.500 ? 947 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.500 _refine_ls_shell.d_res_low 2.565 _refine_ls_shell.number_reflns_R_work 199 _refine_ls_shell.R_factor_R_work 0.268 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.414 _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 199 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3CE5 _struct.title 'A bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule BRACO19' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3CE5 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'bimolecular, parallel, human, telomere, quadruplex, complex, trisubstituted, acridine, BRACO19, 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 2 ? E N N 3 ? F N N 4 ? G N N 4 ? # _struct_biol.id 1 _struct_biol.details 'The second part of the biologically relevant assembly is generated by the operation: -x+1/2, -y+1/2, z+1/2' # 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 metalc1 metalc ? ? A DG 5 O6 ? ? ? 1_555 D K . K ? ? A DG 5 A K 26 1_555 ? ? ? ? ? ? ? 2.563 ? ? metalc2 metalc ? ? A DG 9 O6 ? ? ? 1_555 C K . K ? ? A DG 9 A K 25 1_555 ? ? ? ? ? ? ? 2.760 ? ? metalc3 metalc ? ? A DG 10 O6 ? ? ? 1_555 C K . K ? ? A DG 10 A K 25 1_555 ? ? ? ? ? ? ? 2.874 ? ? metalc4 metalc ? ? C K . K ? ? ? 1_555 B DG 9 O6 ? ? A K 25 B DG 21 1_555 ? ? ? ? ? ? ? 2.845 ? ? metalc5 metalc ? ? C K . K ? ? ? 1_555 B DG 10 O6 ? ? A K 25 B DG 22 1_555 ? ? ? ? ? ? ? 2.933 ? ? metalc6 metalc ? ? D K . K ? ? ? 1_555 B DG 5 O6 ? ? A K 26 B DG 17 1_555 ? ? ? ? ? ? ? 2.846 ? ? metalc7 metalc ? ? D K . K ? ? ? 1_555 B DG 10 O6 ? ? A K 26 B DG 22 1_555 ? ? ? ? ? ? ? 2.888 ? ? metalc8 metalc ? ? D K . K ? ? ? 1_555 B DG 11 O6 ? ? A K 26 B DG 23 1_555 ? ? ? ? ? ? ? 2.824 ? ? hydrog1 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 1 N3 ? ? A DA 2 B DT 13 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog2 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 1 O2 ? ? A DA 2 B DT 13 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog3 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DG 9 O6 ? ? A DG 3 A DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DG 9 N7 ? ? A DG 3 A DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 3 N7 ? ? ? 1_555 B DG 9 N2 ? ? A DG 3 B DG 21 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DG 9 N1 ? ? A DG 3 B DG 21 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DG 10 O6 ? ? A DG 4 A DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DG 10 N7 ? ? A DG 4 A DG 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DG 4 N7 ? ? ? 1_555 B DG 10 N2 ? ? A DG 4 B DG 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DG 10 N1 ? ? A DG 4 B DG 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 A DG 11 O6 ? ? A DG 5 A DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 A DG 11 N7 ? ? A DG 5 A DG 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A DG 5 N7 ? ? ? 1_555 B DG 11 N2 ? ? A DG 5 B DG 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DG 11 N1 ? ? A DG 5 B DG 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DG 3 O6 ? ? A DG 9 B DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DG 3 N7 ? ? A DG 9 B DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog17 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DG 4 O6 ? ? A DG 10 B DG 16 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DG 4 N7 ? ? A DG 10 B DG 16 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DG 5 O6 ? ? A DG 11 B DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog20 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DG 5 N7 ? ? A DG 11 B DG 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog21 hydrog ? ? B DG 3 N1 ? ? ? 1_555 B DG 9 O6 ? ? B DG 15 B DG 21 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog22 hydrog ? ? B DG 3 N2 ? ? ? 1_555 B DG 9 N7 ? ? B DG 15 B DG 21 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog23 hydrog ? ? B DG 4 N1 ? ? ? 1_555 B DG 10 O6 ? ? B DG 16 B DG 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog24 hydrog ? ? B DG 4 N2 ? ? ? 1_555 B DG 10 N7 ? ? B DG 16 B DG 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog25 hydrog ? ? B DG 5 N1 ? ? ? 1_555 B DG 11 O6 ? ? B DG 17 B DG 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog26 hydrog ? ? B DG 5 N2 ? ? ? 1_555 B DG 11 N7 ? ? B DG 17 B DG 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 K 25 ? 8 'BINDING SITE FOR RESIDUE K A 25' AC2 Software A K 26 ? 8 'BINDING SITE FOR RESIDUE K A 26' AC3 Software A BRA 27 ? 11 'BINDING SITE FOR RESIDUE BRA A 27' 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 8 DG A 3 ? DG A 3 . ? 1_555 ? 2 AC1 8 DG A 4 ? DG A 4 . ? 1_555 ? 3 AC1 8 DG A 9 ? DG A 9 . ? 1_555 ? 4 AC1 8 DG A 10 ? DG A 10 . ? 1_555 ? 5 AC1 8 DG B 3 ? DG B 15 . ? 1_555 ? 6 AC1 8 DG B 4 ? DG B 16 . ? 1_555 ? 7 AC1 8 DG B 9 ? DG B 21 . ? 1_555 ? 8 AC1 8 DG B 10 ? DG B 22 . ? 1_555 ? 9 AC2 8 DG A 4 ? DG A 4 . ? 1_555 ? 10 AC2 8 DG A 5 ? DG A 5 . ? 1_555 ? 11 AC2 8 DG A 10 ? DG A 10 . ? 1_555 ? 12 AC2 8 DG A 11 ? DG A 11 . ? 1_555 ? 13 AC2 8 DG B 4 ? DG B 16 . ? 1_555 ? 14 AC2 8 DG B 5 ? DG B 17 . ? 1_555 ? 15 AC2 8 DG B 10 ? DG B 22 . ? 1_555 ? 16 AC2 8 DG B 11 ? DG B 23 . ? 1_555 ? 17 AC3 11 DT A 1 ? DT A 1 . ? 6_555 ? 18 AC3 11 DA A 2 ? DA A 2 . ? 6_555 ? 19 AC3 11 DG A 5 ? DG A 5 . ? 1_555 ? 20 AC3 11 DT A 6 ? DT A 6 . ? 1_555 ? 21 AC3 11 DG A 11 ? DG A 11 . ? 1_555 ? 22 AC3 11 DT A 12 ? DT A 12 . ? 1_555 ? 23 AC3 11 DT B 1 ? DT B 13 . ? 6_555 ? 24 AC3 11 DA B 2 ? DA B 14 . ? 6_555 ? 25 AC3 11 DG B 5 ? DG B 17 . ? 1_555 ? 26 AC3 11 DA B 8 ? DA B 20 . ? 6_555 ? 27 AC3 11 DT B 12 ? DT B 24 . ? 1_555 ? # _database_PDB_matrix.entry_id 3CE5 _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 3CE5 _atom_sites.fract_transf_matrix[1][1] 0.014217 _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] 0.014217 _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] 0.029160 _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 K 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 DT 1 1 1 DT T A . n A 1 2 DA 2 2 2 DA A A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DG 11 11 11 DG G A . n A 1 12 DT 12 12 12 DT T A . n B 1 1 DT 1 13 13 DT T B . n B 1 2 DA 2 14 14 DA A B . n B 1 3 DG 3 15 15 DG G B . n B 1 4 DG 4 16 16 DG G B . n B 1 5 DG 5 17 17 DG G B . n B 1 6 DT 6 18 18 DT T B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DA 8 20 20 DA A B . n B 1 9 DG 9 21 21 DG G B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DG 11 23 23 DG G B . n B 1 12 DT 12 24 24 DT T B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 K 1 25 25 K K A . D 2 K 1 26 26 K K A . E 3 BRA 1 27 1 BRA BRA A . F 4 HOH 1 28 1 HOH HOH A . F 4 HOH 2 29 2 HOH HOH A . F 4 HOH 3 30 3 HOH HOH A . F 4 HOH 4 31 5 HOH HOH A . F 4 HOH 5 32 12 HOH HOH A . F 4 HOH 6 33 13 HOH HOH A . F 4 HOH 7 34 14 HOH HOH A . F 4 HOH 8 35 15 HOH HOH A . F 4 HOH 9 36 19 HOH HOH A . F 4 HOH 10 37 21 HOH HOH A . F 4 HOH 11 38 22 HOH HOH A . F 4 HOH 12 39 23 HOH HOH A . F 4 HOH 13 40 26 HOH HOH A . F 4 HOH 14 41 28 HOH HOH A . F 4 HOH 15 42 29 HOH HOH A . F 4 HOH 16 43 32 HOH HOH A . F 4 HOH 17 44 33 HOH HOH A . F 4 HOH 18 45 34 HOH HOH A . F 4 HOH 19 46 35 HOH HOH A . F 4 HOH 20 47 36 HOH HOH A . F 4 HOH 21 48 37 HOH HOH A . F 4 HOH 22 49 38 HOH HOH A . F 4 HOH 23 50 39 HOH HOH A . F 4 HOH 24 51 40 HOH HOH A . F 4 HOH 25 52 44 HOH HOH A . F 4 HOH 26 53 45 HOH HOH A . F 4 HOH 27 54 46 HOH HOH A . F 4 HOH 28 55 47 HOH HOH A . F 4 HOH 29 56 48 HOH HOH A . F 4 HOH 30 57 49 HOH HOH A . F 4 HOH 31 58 52 HOH HOH A . F 4 HOH 32 59 53 HOH HOH A . F 4 HOH 33 60 54 HOH HOH A . G 4 HOH 1 25 4 HOH HOH B . G 4 HOH 2 26 6 HOH HOH B . G 4 HOH 3 27 7 HOH HOH B . G 4 HOH 4 28 8 HOH HOH B . G 4 HOH 5 29 9 HOH HOH B . G 4 HOH 6 30 10 HOH HOH B . G 4 HOH 7 31 11 HOH HOH B . G 4 HOH 8 32 16 HOH HOH B . G 4 HOH 9 33 17 HOH HOH B . G 4 HOH 10 34 18 HOH HOH B . G 4 HOH 11 35 20 HOH HOH B . G 4 HOH 12 36 24 HOH HOH B . G 4 HOH 13 37 25 HOH HOH B . G 4 HOH 14 38 27 HOH HOH B . G 4 HOH 15 39 30 HOH HOH B . G 4 HOH 16 40 31 HOH HOH B . G 4 HOH 17 41 41 HOH HOH B . G 4 HOH 18 42 42 HOH HOH B . G 4 HOH 19 43 43 HOH HOH B . G 4 HOH 20 44 50 HOH HOH B . G 4 HOH 21 45 51 HOH HOH B . # _struct_site_keywords.site_id 1 _struct_site_keywords.text intercalation # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? tetrameric 4 2 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,B,C,D,E,F,G 2 1 A,B,C,D,E,F,G # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 2 'ABSA (A^2)' 1830 ? 2 MORE -9.0 ? 2 'SSA (A^2)' 4640 ? # 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' 6_555 -x+1/2,-y+1/2,z+1/2 -1.0000000000 0.0000000000 0.0000000000 35.1690000000 0.0000000000 -1.0000000000 0.0000000000 35.1690000000 0.0000000000 0.0000000000 1.0000000000 17.1465000000 # 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 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? D K . ? A K 26 ? 1_555 O6 ? B DG 5 ? B DG 17 ? 1_555 114.0 ? 2 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? D K . ? A K 26 ? 1_555 O6 ? B DG 10 ? B DG 22 ? 1_555 137.3 ? 3 O6 ? B DG 5 ? B DG 17 ? 1_555 K ? D K . ? A K 26 ? 1_555 O6 ? B DG 10 ? B DG 22 ? 1_555 89.9 ? 4 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? D K . ? A K 26 ? 1_555 O6 ? B DG 11 ? B DG 23 ? 1_555 75.5 ? 5 O6 ? B DG 5 ? B DG 17 ? 1_555 K ? D K . ? A K 26 ? 1_555 O6 ? B DG 11 ? B DG 23 ? 1_555 79.6 ? 6 O6 ? B DG 10 ? B DG 22 ? 1_555 K ? D K . ? A K 26 ? 1_555 O6 ? B DG 11 ? B DG 23 ? 1_555 74.9 ? 7 O6 ? A DG 9 ? A DG 9 ? 1_555 K ? C K . ? A K 25 ? 1_555 O6 ? A DG 10 ? A DG 10 ? 1_555 78.4 ? 8 O6 ? A DG 9 ? A DG 9 ? 1_555 K ? C K . ? A K 25 ? 1_555 O6 ? B DG 9 ? B DG 21 ? 1_555 122.3 ? 9 O6 ? A DG 10 ? A DG 10 ? 1_555 K ? C K . ? A K 25 ? 1_555 O6 ? B DG 9 ? B DG 21 ? 1_555 146.8 ? 10 O6 ? A DG 9 ? A DG 9 ? 1_555 K ? C K . ? A K 25 ? 1_555 O6 ? B DG 10 ? B DG 22 ? 1_555 153.1 ? 11 O6 ? A DG 10 ? A DG 10 ? 1_555 K ? C K . ? A K 25 ? 1_555 O6 ? B DG 10 ? B DG 22 ? 1_555 106.2 ? 12 O6 ? B DG 9 ? B DG 21 ? 1_555 K ? C K . ? A K 25 ? 1_555 O6 ? B DG 10 ? B DG 22 ? 1_555 67.8 ? # 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 2008-05-13 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-01-11 4 'Structure model' 1 3 2023-08-30 # _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' Other 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_ref_seq 7 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_dist_value' 4 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 5 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 18 4 'Structure model' '_struct_ref_seq.db_align_beg' 19 4 'Structure model' '_struct_ref_seq.db_align_end' 20 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 21 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 22 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 CrystalClear 'data collection' . ? 2 d*TREK 'data reduction' . ? 3 d*TREK 'data scaling' . ? 4 PHASER phasing . ? 5 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C5'" A DT 1 ? ? "C4'" A DT 1 ? ? 1.563 1.512 0.051 0.007 N 2 1 "O3'" A DT 1 ? ? "C3'" A DT 1 ? ? 1.556 1.435 0.121 0.013 N 3 1 "C5'" A DA 2 ? ? "C4'" A DA 2 ? ? 1.554 1.512 0.042 0.007 N 4 1 "O3'" A DT 12 ? ? "C3'" A DT 12 ? ? 1.359 1.419 -0.060 0.006 N 5 1 C2 A DT 12 ? ? O2 A DT 12 ? ? 1.165 1.220 -0.055 0.008 N 6 1 C4 A DT 12 ? ? O4 A DT 12 ? ? 1.173 1.228 -0.055 0.009 N 7 1 C2 B DT 13 ? ? O2 B DT 13 ? ? 1.168 1.220 -0.052 0.008 N 8 1 "O3'" B DG 16 ? ? "C3'" B DG 16 ? ? 1.341 1.419 -0.078 0.006 N 9 1 "O3'" B DT 24 ? ? "C3'" B DT 24 ? ? 1.337 1.419 -0.082 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 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 111.81 108.30 3.51 0.30 N 2 1 "C3'" A DT 1 ? ? "O3'" A DT 1 ? ? P A DA 2 ? B 129.19 119.70 9.49 1.20 Y 3 1 P A DA 2 ? A "O5'" A DA 2 ? ? "C5'" A DA 2 ? ? 133.20 120.90 12.30 1.60 N 4 1 "O4'" A DG 3 ? ? "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? 102.05 104.50 -2.45 0.40 N 5 1 C5 A DG 3 ? ? C6 A DG 3 ? ? N1 A DG 3 ? ? 115.40 111.50 3.90 0.50 N 6 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 111.29 108.30 2.99 0.30 N 7 1 C2 A DG 5 ? ? N3 A DG 5 ? ? C4 A DG 5 ? ? 116.12 111.90 4.22 0.50 N 8 1 N1 A DG 5 ? ? C6 A DG 5 ? ? O6 A DG 5 ? ? 115.86 119.90 -4.04 0.60 N 9 1 N1 A DT 6 ? ? C2 A DT 6 ? ? N3 A DT 6 ? ? 118.37 114.60 3.77 0.60 N 10 1 C2 A DT 6 ? ? N3 A DT 6 ? ? C4 A DT 6 ? ? 122.71 127.20 -4.49 0.60 N 11 1 N1 A DT 6 ? ? C2 A DT 6 ? ? O2 A DT 6 ? ? 117.73 123.10 -5.37 0.80 N 12 1 C5 A DT 6 ? ? C4 A DT 6 ? ? O4 A DT 6 ? ? 120.61 124.90 -4.29 0.70 N 13 1 "O4'" A DT 7 ? ? "C4'" A DT 7 ? ? "C3'" A DT 7 ? ? 101.41 104.50 -3.09 0.40 N 14 1 N3 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 125.59 119.90 5.69 0.60 N 15 1 C5 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 120.54 124.90 -4.36 0.70 N 16 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? "C2'" A DA 8 ? ? 99.38 105.90 -6.52 0.80 N 17 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 102.84 108.00 -5.16 0.70 N 18 1 C6 A DA 8 ? ? N1 A DA 8 ? ? C2 A DA 8 ? ? 112.94 118.60 -5.66 0.60 N 19 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N1 A DA 8 ? ? 120.75 117.70 3.05 0.50 N 20 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N6 A DA 8 ? ? 118.25 123.70 -5.45 0.80 N 21 1 C2 A DG 9 ? ? N3 A DG 9 ? ? C4 A DG 9 ? ? 116.07 111.90 4.17 0.50 N 22 1 N1 A DG 9 ? ? C2 A DG 9 ? ? N2 A DG 9 ? ? 122.10 116.20 5.90 0.90 N 23 1 C5 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 124.66 128.60 -3.94 0.60 N 24 1 C6 A DG 10 ? ? N1 A DG 10 ? ? C2 A DG 10 ? ? 119.74 125.10 -5.36 0.60 N 25 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 115.78 111.50 4.28 0.50 N 26 1 N1 A DG 10 ? ? C6 A DG 10 ? ? O6 A DG 10 ? ? 115.56 119.90 -4.34 0.60 N 27 1 "O4'" A DG 11 ? ? "C4'" A DG 11 ? ? "C3'" A DG 11 ? ? 99.20 104.50 -5.30 0.40 N 28 1 C2 A DG 11 ? ? N3 A DG 11 ? ? C4 A DG 11 ? ? 115.40 111.90 3.50 0.50 N 29 1 "O4'" A DT 12 ? ? "C1'" A DT 12 ? ? "C2'" A DT 12 ? ? 95.86 105.90 -10.04 0.80 N 30 1 "O4'" A DT 12 ? ? "C1'" A DT 12 ? ? N1 A DT 12 ? ? 101.63 108.00 -6.37 0.70 N 31 1 C6 A DT 12 ? ? N1 A DT 12 ? ? C2 A DT 12 ? ? 117.15 121.30 -4.15 0.50 N 32 1 N1 A DT 12 ? ? C2 A DT 12 ? ? N3 A DT 12 ? ? 119.96 114.60 5.36 0.60 N 33 1 C2 A DT 12 ? ? N3 A DT 12 ? ? C4 A DT 12 ? ? 121.87 127.20 -5.33 0.60 N 34 1 N3 A DT 12 ? ? C2 A DT 12 ? ? O2 A DT 12 ? ? 115.66 122.30 -6.64 0.60 N 35 1 C5 A DT 12 ? ? C4 A DT 12 ? ? O4 A DT 12 ? ? 118.27 124.90 -6.63 0.70 N 36 1 "C1'" B DT 13 ? ? "O4'" B DT 13 ? ? "C4'" B DT 13 ? ? 115.96 110.30 5.66 0.70 N 37 1 "O4'" B DT 13 ? ? "C1'" B DT 13 ? ? "C2'" B DT 13 ? ? 100.03 105.90 -5.87 0.80 N 38 1 C6 B DT 13 ? ? N1 B DT 13 ? ? C2 B DT 13 ? ? 117.19 121.30 -4.11 0.50 N 39 1 "C1'" B DA 14 ? ? "O4'" B DA 14 ? ? "C4'" B DA 14 ? ? 114.67 110.30 4.37 0.70 N 40 1 "O4'" B DA 14 ? ? "C1'" B DA 14 ? ? "C2'" B DA 14 ? ? 99.14 105.90 -6.76 0.80 N 41 1 C4 B DG 16 ? ? C5 B DG 16 ? ? N7 B DG 16 ? ? 113.37 110.80 2.57 0.40 N 42 1 C5 B DG 16 ? ? N7 B DG 16 ? ? C8 B DG 16 ? ? 100.69 104.30 -3.61 0.50 N 43 1 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 102.76 108.00 -5.24 0.70 N 44 1 N3 B DT 19 ? ? C4 B DT 19 ? ? O4 B DT 19 ? ? 123.97 119.90 4.07 0.60 N 45 1 C5 B DT 19 ? ? C4 B DT 19 ? ? O4 B DT 19 ? ? 120.34 124.90 -4.56 0.70 N 46 1 C4 B DT 19 ? ? C5 B DT 19 ? ? C7 B DT 19 ? ? 114.82 119.00 -4.18 0.60 N 47 1 C6 B DT 19 ? ? C5 B DT 19 ? ? C7 B DT 19 ? ? 126.74 122.90 3.84 0.60 N 48 1 C4 B DA 20 ? ? C5 B DA 20 ? ? N7 B DA 20 ? ? 114.69 110.70 3.99 0.50 N 49 1 C5 B DA 20 ? ? N7 B DA 20 ? ? C8 B DA 20 ? ? 100.31 103.90 -3.59 0.50 N 50 1 N1 B DA 20 ? ? C6 B DA 20 ? ? N6 B DA 20 ? ? 123.90 118.60 5.30 0.60 N 51 1 C5 B DA 20 ? ? C6 B DA 20 ? ? N6 B DA 20 ? ? 117.27 123.70 -6.43 0.80 N 52 1 OP1 B DG 21 ? ? P B DG 21 ? ? OP2 B DG 21 ? ? 129.96 119.60 10.36 1.50 N 53 1 C5 B DG 21 ? ? C6 B DG 21 ? ? N1 B DG 21 ? ? 114.65 111.50 3.15 0.50 N 54 1 C5 B DG 23 ? ? C6 B DG 23 ? ? N1 B DG 23 ? ? 114.99 111.50 3.49 0.50 N 55 1 "O4'" B DT 24 ? ? "C4'" B DT 24 ? ? "C3'" B DT 24 ? ? 101.60 104.50 -2.90 0.40 N 56 1 N3 B DT 24 ? ? C4 B DT 24 ? ? C5 B DT 24 ? ? 119.26 115.20 4.06 0.60 N 57 1 C5 B DT 24 ? ? C4 B DT 24 ? ? O4 B DT 24 ? ? 118.24 124.90 -6.66 0.70 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 BRA C40 C N N 1 BRA C41 C N N 2 BRA C42 C N N 3 BRA C43 C N N 4 BRA N39 N N N 5 BRA C38 C N N 6 BRA C37 C N N 7 BRA C36 C N N 8 BRA O52 O N N 9 BRA N17 N N N 10 BRA C3 C Y N 11 BRA C4 C Y N 12 BRA C2 C Y N 13 BRA C1 C Y N 14 BRA C6 C Y N 15 BRA C10 C Y N 16 BRA N19 N N N 17 BRA C28 C Y N 18 BRA C29 C Y N 19 BRA C24 C Y N 20 BRA C25 C Y N 21 BRA N15 N N N 22 BRA C16 C N N 23 BRA C18 C N N 24 BRA C26 C Y N 25 BRA C27 C Y N 26 BRA C5 C Y N 27 BRA N7 N Y N 28 BRA C8 C Y N 29 BRA C11 C Y N 30 BRA C9 C Y N 31 BRA C14 C Y N 32 BRA C13 C Y N 33 BRA C12 C Y N 34 BRA N21 N N N 35 BRA C44 C N N 36 BRA O53 O N N 37 BRA C45 C N N 38 BRA C46 C N N 39 BRA N47 N N N 40 BRA C48 C N N 41 BRA C49 C N N 42 BRA C50 C N N 43 BRA C51 C N N 44 BRA H40 H N N 45 BRA H40A H N N 46 BRA H41 H N N 47 BRA H41A H N N 48 BRA H42 H N N 49 BRA H42A H N N 50 BRA H43 H N N 51 BRA H43A H N N 52 BRA H38 H N N 53 BRA H38A H N N 54 BRA H37 H N N 55 BRA H37A H N N 56 BRA HN17 H N N 57 BRA H4 H N N 58 BRA H2 H N N 59 BRA H1 H N N 60 BRA HN19 H N N 61 BRA H29 H N N 62 BRA H24 H N N 63 BRA H16 H N N 64 BRA H16A H N N 65 BRA H16B H N N 66 BRA H18 H N N 67 BRA H18A H N N 68 BRA H18B H N N 69 BRA H26 H N N 70 BRA H27 H N N 71 BRA H11 H N N 72 BRA H14 H N N 73 BRA H13 H N N 74 BRA HN21 H N N 75 BRA H45 H N N 76 BRA H45A H N N 77 BRA H46 H N N 78 BRA H46A H N N 79 BRA H48 H N N 80 BRA H48A H N N 81 BRA H49 H N N 82 BRA H49A H N N 83 BRA H50 H N N 84 BRA H50A H N N 85 BRA H51 H N N 86 BRA H51A H N N 87 DA OP3 O N N 88 DA P P N N 89 DA OP1 O N N 90 DA OP2 O N N 91 DA "O5'" O N N 92 DA "C5'" C N N 93 DA "C4'" C N R 94 DA "O4'" O N N 95 DA "C3'" C N S 96 DA "O3'" O N N 97 DA "C2'" C N N 98 DA "C1'" C N R 99 DA N9 N Y N 100 DA C8 C Y N 101 DA N7 N Y N 102 DA C5 C Y N 103 DA C6 C Y N 104 DA N6 N N N 105 DA N1 N Y N 106 DA C2 C Y N 107 DA N3 N Y N 108 DA C4 C Y N 109 DA HOP3 H N N 110 DA HOP2 H N N 111 DA "H5'" H N N 112 DA "H5''" H N N 113 DA "H4'" H N N 114 DA "H3'" H N N 115 DA "HO3'" H N N 116 DA "H2'" H N N 117 DA "H2''" H N N 118 DA "H1'" H N N 119 DA H8 H N N 120 DA H61 H N N 121 DA H62 H N N 122 DA H2 H N N 123 DG OP3 O N N 124 DG P P N N 125 DG OP1 O N N 126 DG OP2 O N N 127 DG "O5'" O N N 128 DG "C5'" C N N 129 DG "C4'" C N R 130 DG "O4'" O N N 131 DG "C3'" C N S 132 DG "O3'" O N N 133 DG "C2'" C N N 134 DG "C1'" C N R 135 DG N9 N Y N 136 DG C8 C Y N 137 DG N7 N Y N 138 DG C5 C Y N 139 DG C6 C N N 140 DG O6 O N N 141 DG N1 N N N 142 DG C2 C N N 143 DG N2 N N N 144 DG N3 N N N 145 DG C4 C Y N 146 DG HOP3 H N N 147 DG HOP2 H N N 148 DG "H5'" H N N 149 DG "H5''" H N N 150 DG "H4'" H N N 151 DG "H3'" H N N 152 DG "HO3'" H N N 153 DG "H2'" H N N 154 DG "H2''" H N N 155 DG "H1'" H N N 156 DG H8 H N N 157 DG H1 H N N 158 DG H21 H N N 159 DG H22 H N N 160 DT OP3 O N N 161 DT P P N N 162 DT OP1 O N N 163 DT OP2 O N N 164 DT "O5'" O N N 165 DT "C5'" C N N 166 DT "C4'" C N R 167 DT "O4'" O N N 168 DT "C3'" C N S 169 DT "O3'" O N N 170 DT "C2'" C N N 171 DT "C1'" C N R 172 DT N1 N N N 173 DT C2 C N N 174 DT O2 O N N 175 DT N3 N N N 176 DT C4 C N N 177 DT O4 O N N 178 DT C5 C N N 179 DT C7 C N N 180 DT C6 C N N 181 DT HOP3 H N N 182 DT HOP2 H N N 183 DT "H5'" H N N 184 DT "H5''" H N N 185 DT "H4'" H N N 186 DT "H3'" H N N 187 DT "HO3'" H N N 188 DT "H2'" H N N 189 DT "H2''" H N N 190 DT "H1'" H N N 191 DT H3 H N N 192 DT H71 H N N 193 DT H72 H N N 194 DT H73 H N N 195 DT H6 H N N 196 HOH O O N N 197 HOH H1 H N N 198 HOH H2 H N N 199 K K K N N 200 # 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 BRA C40 N39 sing N N 1 BRA C40 C41 sing N N 2 BRA C40 H40 sing N N 3 BRA C40 H40A sing N N 4 BRA C42 C41 sing N N 5 BRA C41 H41 sing N N 6 BRA C41 H41A sing N N 7 BRA C43 C42 sing N N 8 BRA C42 H42 sing N N 9 BRA C42 H42A sing N N 10 BRA C43 N39 sing N N 11 BRA C43 H43 sing N N 12 BRA C43 H43A sing N N 13 BRA C38 N39 sing N N 14 BRA C38 C37 sing N N 15 BRA C38 H38 sing N N 16 BRA C38 H38A sing N N 17 BRA C36 C37 sing N N 18 BRA C37 H37 sing N N 19 BRA C37 H37A sing N N 20 BRA N17 C36 sing N N 21 BRA C36 O52 doub N N 22 BRA C3 N17 sing N N 23 BRA N17 HN17 sing N N 24 BRA C4 C3 doub Y N 25 BRA C3 C2 sing Y N 26 BRA C5 C4 sing Y N 27 BRA C4 H4 sing N N 28 BRA C1 C2 doub Y N 29 BRA C2 H2 sing N N 30 BRA C6 C1 sing Y N 31 BRA C1 H1 sing N N 32 BRA C5 C6 sing Y N 33 BRA C10 C6 doub Y N 34 BRA C9 C10 sing Y N 35 BRA C10 N19 sing N N 36 BRA C28 N19 sing N N 37 BRA N19 HN19 sing N N 38 BRA C29 C28 doub Y N 39 BRA C28 C27 sing Y N 40 BRA C24 C29 sing Y N 41 BRA C29 H29 sing N N 42 BRA C24 C25 doub Y N 43 BRA C24 H24 sing N N 44 BRA N15 C25 sing N N 45 BRA C25 C26 sing Y N 46 BRA C18 N15 sing N N 47 BRA N15 C16 sing N N 48 BRA C16 H16 sing N N 49 BRA C16 H16A sing N N 50 BRA C16 H16B sing N N 51 BRA C18 H18 sing N N 52 BRA C18 H18A sing N N 53 BRA C18 H18B sing N N 54 BRA C26 C27 doub Y N 55 BRA C26 H26 sing N N 56 BRA C27 H27 sing N N 57 BRA N7 C5 doub Y N 58 BRA N7 C8 sing Y N 59 BRA C11 C8 doub Y N 60 BRA C8 C9 sing Y N 61 BRA C11 C12 sing Y N 62 BRA C11 H11 sing N N 63 BRA C14 C9 doub Y N 64 BRA C13 C14 sing Y N 65 BRA C14 H14 sing N N 66 BRA C12 C13 doub Y N 67 BRA C13 H13 sing N N 68 BRA N21 C12 sing N N 69 BRA C44 N21 sing N N 70 BRA N21 HN21 sing N N 71 BRA O53 C44 doub N N 72 BRA C45 C44 sing N N 73 BRA C46 C45 sing N N 74 BRA C45 H45 sing N N 75 BRA C45 H45A sing N N 76 BRA N47 C46 sing N N 77 BRA C46 H46 sing N N 78 BRA C46 H46A sing N N 79 BRA C48 N47 sing N N 80 BRA N47 C51 sing N N 81 BRA C48 C49 sing N N 82 BRA C48 H48 sing N N 83 BRA C48 H48A sing N N 84 BRA C49 C50 sing N N 85 BRA C49 H49 sing N N 86 BRA C49 H49A sing N N 87 BRA C50 C51 sing N N 88 BRA C50 H50 sing N N 89 BRA C50 H50A sing N N 90 BRA C51 H51 sing N N 91 BRA C51 H51A sing N N 92 DA OP3 P sing N N 93 DA OP3 HOP3 sing N N 94 DA P OP1 doub N N 95 DA P OP2 sing N N 96 DA P "O5'" sing N N 97 DA OP2 HOP2 sing N N 98 DA "O5'" "C5'" sing N N 99 DA "C5'" "C4'" sing N N 100 DA "C5'" "H5'" sing N N 101 DA "C5'" "H5''" sing N N 102 DA "C4'" "O4'" sing N N 103 DA "C4'" "C3'" sing N N 104 DA "C4'" "H4'" sing N N 105 DA "O4'" "C1'" sing N N 106 DA "C3'" "O3'" sing N N 107 DA "C3'" "C2'" sing N N 108 DA "C3'" "H3'" sing N N 109 DA "O3'" "HO3'" sing N N 110 DA "C2'" "C1'" sing N N 111 DA "C2'" "H2'" sing N N 112 DA "C2'" "H2''" sing N N 113 DA "C1'" N9 sing N N 114 DA "C1'" "H1'" sing N N 115 DA N9 C8 sing Y N 116 DA N9 C4 sing Y N 117 DA C8 N7 doub Y N 118 DA C8 H8 sing N N 119 DA N7 C5 sing Y N 120 DA C5 C6 sing Y N 121 DA C5 C4 doub Y N 122 DA C6 N6 sing N N 123 DA C6 N1 doub Y N 124 DA N6 H61 sing N N 125 DA N6 H62 sing N N 126 DA N1 C2 sing Y N 127 DA C2 N3 doub Y N 128 DA C2 H2 sing N N 129 DA N3 C4 sing Y N 130 DG OP3 P sing N N 131 DG OP3 HOP3 sing N N 132 DG P OP1 doub N N 133 DG P OP2 sing N N 134 DG P "O5'" sing N N 135 DG OP2 HOP2 sing N N 136 DG "O5'" "C5'" sing N N 137 DG "C5'" "C4'" sing N N 138 DG "C5'" "H5'" sing N N 139 DG "C5'" "H5''" sing N N 140 DG "C4'" "O4'" sing N N 141 DG "C4'" "C3'" sing N N 142 DG "C4'" "H4'" sing N N 143 DG "O4'" "C1'" sing N N 144 DG "C3'" "O3'" sing N N 145 DG "C3'" "C2'" sing N N 146 DG "C3'" "H3'" sing N N 147 DG "O3'" "HO3'" sing N N 148 DG "C2'" "C1'" sing N N 149 DG "C2'" "H2'" sing N N 150 DG "C2'" "H2''" sing N N 151 DG "C1'" N9 sing N N 152 DG "C1'" "H1'" sing N N 153 DG N9 C8 sing Y N 154 DG N9 C4 sing Y N 155 DG C8 N7 doub Y N 156 DG C8 H8 sing N N 157 DG N7 C5 sing Y N 158 DG C5 C6 sing N N 159 DG C5 C4 doub Y N 160 DG C6 O6 doub N N 161 DG C6 N1 sing N N 162 DG N1 C2 sing N N 163 DG N1 H1 sing N N 164 DG C2 N2 sing N N 165 DG C2 N3 doub N N 166 DG N2 H21 sing N N 167 DG N2 H22 sing N N 168 DG N3 C4 sing N N 169 DT OP3 P sing N N 170 DT OP3 HOP3 sing N N 171 DT P OP1 doub N N 172 DT P OP2 sing N N 173 DT P "O5'" sing N N 174 DT OP2 HOP2 sing N N 175 DT "O5'" "C5'" sing N N 176 DT "C5'" "C4'" sing N N 177 DT "C5'" "H5'" sing N N 178 DT "C5'" "H5''" sing N N 179 DT "C4'" "O4'" sing N N 180 DT "C4'" "C3'" sing N N 181 DT "C4'" "H4'" sing N N 182 DT "O4'" "C1'" sing N N 183 DT "C3'" "O3'" sing N N 184 DT "C3'" "C2'" sing N N 185 DT "C3'" "H3'" sing N N 186 DT "O3'" "HO3'" sing N N 187 DT "C2'" "C1'" sing N N 188 DT "C2'" "H2'" sing N N 189 DT "C2'" "H2''" sing N N 190 DT "C1'" N1 sing N N 191 DT "C1'" "H1'" sing N N 192 DT N1 C2 sing N N 193 DT N1 C6 sing N N 194 DT C2 O2 doub N N 195 DT C2 N3 sing N N 196 DT N3 C4 sing N N 197 DT N3 H3 sing N N 198 DT C4 O4 doub N N 199 DT C4 C5 sing N N 200 DT C5 C7 sing N N 201 DT C5 C6 doub N N 202 DT C7 H71 sing N N 203 DT C7 H72 sing N N 204 DT C7 H73 sing N N 205 DT C6 H6 sing N N 206 HOH O H1 sing N N 207 HOH O H2 sing N N 208 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3CE5 'double helix' 3CE5 'parallel strands' 3CE5 '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 DA 2 1_555 B DT 1 1_555 0.076 1.216 -0.085 8.942 -12.694 176.421 1 A_DA2:DT13_B A 2 ? B 13 ? 21 2 1 A DG 3 1_555 A DG 9 1_555 1.910 3.388 -0.152 -4.479 -0.410 -88.532 2 A_DG3:DG9_A A 3 ? A 9 ? 6 3 1 B DG 9 1_555 B DG 3 1_555 -2.031 -3.174 0.492 -0.098 1.361 90.324 3 B_DG21:DG15_B B 21 ? B 15 ? 6 3 1 A DG 10 1_555 B DG 4 1_555 1.760 3.581 -0.128 -2.093 -6.608 -90.372 4 A_DG10:DG16_B A 10 ? B 16 ? 6 3 1 A DG 4 1_555 B DG 10 1_555 -1.840 -3.142 0.174 -1.518 9.462 88.696 5 A_DG4:DG22_B A 4 ? B 22 ? 6 3 1 A DG 5 1_555 A DG 11 1_555 1.724 2.637 -0.033 6.350 -10.786 -98.660 6 A_DG5:DG11_A A 5 ? A 11 ? 6 3 1 B DG 11 1_555 B DG 5 1_555 -1.990 -3.410 0.230 -9.833 7.927 87.102 7 B_DG23:DG17_B B 23 ? B 17 ? 6 3 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DA 2 1_555 B DT 1 1_555 A DG 3 1_555 A DG 9 1_555 1.125 -0.501 2.783 -0.869 2.534 167.788 -0.255 -0.567 2.781 1.274 0.437 167.791 1 AA_DA2DG3:DG9DT13_AB A 2 ? B 13 ? A 3 ? A 9 ? 1 A DG 3 1_555 A DG 9 1_555 B DG 9 1_555 B DG 3 1_555 2.056 3.034 0.221 -0.788 -9.266 -178.928 -1.517 1.028 0.224 4.633 -0.394 -178.932 2 AB_DG3DG21:DG15DG9_BA A 3 ? A 9 ? B 21 ? B 15 ? 1 B DG 9 1_555 B DG 3 1_555 A DG 10 1_555 B DG 4 1_555 0.644 1.840 3.141 -1.217 0.021 -65.623 -1.698 0.546 3.151 -0.019 -1.123 -65.633 3 BA_DG21DG10:DG16DG15_BB B 21 ? B 15 ? A 10 ? B 16 ? 1 A DG 10 1_555 B DG 4 1_555 A DG 4 1_555 B DG 10 1_555 1.790 3.542 -0.058 4.110 -4.693 -177.932 -1.772 0.895 -0.057 2.347 2.055 -177.935 4 AA_DG10DG4:DG22DG16_BB A 10 ? B 16 ? A 4 ? B 22 ? 1 A DG 5 1_555 A DG 11 1_555 B DG 11 1_555 B DG 5 1_555 -1.974 -3.404 -0.276 -2.801 8.112 178.801 -1.702 0.987 -0.278 4.056 1.401 178.805 5 AB_DG5DG23:DG17DG11_BA A 5 ? A 11 ? B 23 ? B 17 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'POTASSIUM ION' K 3 '9-[4-(n,n-dimethylamino)phenylamino]-3,6-bis(3-pyrrolidinopropionamido) acridine' BRA 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 1K8P _pdbx_initial_refinement_model.details 'PDB Entry 1K8P' #