data_4D9Y # _entry.id 4D9Y # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4D9Y pdb_00004d9y 10.2210/pdb4d9y/pdb NDB NA1542 ? ? RCSB RCSB070067 ? ? WWPDB D_1000070067 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3NP6 'The same sequence complexed with Berberine' unspecified PDB 3NX5 'The same sequence complexed with Sanguinarine' unspecified PDB 4D9X 'The same sequence complexed with Coptisine' unspecified # _pdbx_database_status.entry_id 4D9Y _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-01-12 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ferraroni, M.' 1 'Bazzicalupi, C.' 2 'Gratteri, P.' 3 'Bilia, A.R.' 4 # _citation.id primary _citation.title 'The crystal structure of Chelerythrine bound to DNA d(CGTACG)' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ferraroni, M.' 1 ? primary 'Bazzicalupi, C.' 2 ? primary 'Gratteri, P.' 3 ? primary 'Bilia, A.R.' 4 ? # _cell.entry_id 4D9Y _cell.length_a 30.231 _cell.length_b 30.231 _cell.length_c 119.247 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 24 _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 4D9Y _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _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(*CP*GP*TP*AP*CP*G)-3') ; 1809.217 4 ? ? ? ? 2 non-polymer syn '1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium' 348.372 1 ? ? ? ? 3 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 4 water nat water 18.015 11 ? ? ? ? # _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 '(DC)(DG)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _entity_poly.pdbx_strand_id A,B,C,D _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 DT n 1 4 DA n 1 5 DC n 1 6 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 4D9Y _struct_ref.pdbx_db_accession 4D9Y _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CGTACG _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 4D9Y A 1 ? 6 ? 4D9Y 101 ? 106 ? 101 106 2 1 4D9Y B 1 ? 6 ? 4D9Y 207 ? 212 ? 207 212 3 1 4D9Y C 1 ? 6 ? 4D9Y 301 ? 306 ? 301 306 4 1 4D9Y D 1 ? 6 ? 4D9Y 407 ? 412 ? 407 412 # 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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 CTI non-polymer . '1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium' chelerythrine 'C21 H18 N O4 1' 348.372 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 # _exptl.entry_id 4D9Y _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.19 _exptl_crystal.density_percent_sol 43.89 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 296 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'MPD, MgCl2, NaCl, KCL, spermine, pH 6.5, VAPOR DIFFUSION, temperature 296K' # _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 'PILATUS 2M' _diffrn_detector.pdbx_collection_date 2011-03-13 _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 'double-crystal Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ELETTRA BEAMLINE 5.2R' _diffrn_source.pdbx_synchrotron_site ELETTRA _diffrn_source.pdbx_synchrotron_beamline 5.2R _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.000 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4D9Y _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30.0 _reflns.d_resolution_high 2.100 _reflns.number_obs 4087 _reflns.number_all ? _reflns.percent_possible_obs 99.000 _reflns.pdbx_Rmerge_I_obs 0.089 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 13.390 _reflns.B_iso_Wilson_estimate 46.830 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _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 1 1 2.100 2.230 97.800 0.226 ? 5.340 ? ? ? ? ? ? ? 1 2 2.230 2.380 99.700 0.187 ? 7.620 ? ? ? ? ? ? ? 1 3 2.380 2.570 98.900 0.117 ? 12.230 ? ? ? ? ? ? ? 1 4 2.570 2.810 99.000 0.111 ? 14.290 ? ? ? ? ? ? ? 1 5 2.810 3.140 99.400 0.092 ? 16.980 ? ? ? ? ? ? ? 1 6 3.140 3.630 99.300 0.089 ? 18.840 ? ? ? ? ? ? ? 1 7 3.630 4.430 99.500 0.085 ? 19.330 ? ? ? ? ? ? ? 1 8 4.430 6.230 99.300 0.078 ? 18.790 ? ? ? ? ? ? ? 1 9 6.230 30.0 97.900 0.083 ? 17.570 ? ? ? ? ? ? ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4D9Y _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 4087 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.0 _refine.ls_d_res_high 2.10 _refine.ls_percent_reflns_obs 93.9 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2196 _refine.ls_R_factor_R_free 0.3140 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 209 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 1.000 _refine.occupancy_max 1.000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 54.1262 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details 'Crystal was merohedrally twinned with a fraction of 0.46 and twin law -h, -k, l' _refine.pdbx_starting_model 'PDB ENTRY 3NP6' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details 'Reflections were chosen in thin resolution shells' _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _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_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 450 _refine_hist.pdbx_number_atoms_ligand 27 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 488 _refine_hist.d_res_high 2.10 _refine_hist.d_res_low 20.0 # 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 s_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.026 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.005 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.10 _refine_ls_shell.d_res_low 2.19 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.373 _refine_ls_shell.percent_reflns_obs 85.29 _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 4D9Y _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.2196 _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? # _struct.entry_id 4D9Y _struct.title 'The crystal structure of Chelerythrine bound to DNA d(CGTACG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4D9Y _struct_keywords.text 'DRUG-DNA COMPLEX, DOUBLE HELIX, DNA' _struct_keywords.pdbx_keywords 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 1 ? D N N 1 ? E N N 2 ? F N N 3 ? G N N 4 ? H N N 4 ? I N N 4 ? J 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 metalc1 metalc ? ? B DG 6 OP1 ? ? ? 1_555 F CA . CA ? ? B DG 212 B CA 501 1_555 ? ? ? ? ? ? ? 2.215 ? ? metalc2 metalc ? ? F CA . CA ? ? ? 1_555 D DG 6 OP1 ? ? B CA 501 D DG 412 1_555 ? ? ? ? ? ? ? 2.269 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 102 B DC 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 102 B DC 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 102 B DC 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N2 ? ? ? 1_555 D DG 6 N3 ? ? A DG 102 D DG 412 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog5 hydrog ? ? A DG 2 N3 ? ? ? 1_555 D DG 6 N2 ? ? A DG 102 D DG 412 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog6 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 103 B DA 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 103 B DA 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 104 B DT 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 104 B DT 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 105 B DG 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 105 B DG 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 105 B DG 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B DG 6 N2 ? ? ? 1_555 C DG 2 N3 ? ? B DG 212 C DG 302 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog14 hydrog ? ? B DG 6 N3 ? ? ? 1_555 C DG 2 N2 ? ? B DG 212 C DG 302 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog15 hydrog ? ? C DG 2 N1 ? ? ? 1_555 D DC 5 N3 ? ? C DG 302 D DC 411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? C DG 2 N2 ? ? ? 1_555 D DC 5 O2 ? ? C DG 302 D DC 411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? C DG 2 O6 ? ? ? 1_555 D DC 5 N4 ? ? C DG 302 D DC 411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? C DT 3 N3 ? ? ? 1_555 D DA 4 N1 ? ? C DT 303 D DA 410 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? C DT 3 O4 ? ? ? 1_555 D DA 4 N6 ? ? C DT 303 D DA 410 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? C DA 4 N1 ? ? ? 1_555 D DT 3 N3 ? ? C DA 304 D DT 409 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog21 hydrog ? ? C DC 5 N3 ? ? ? 1_555 D DG 2 N1 ? ? C DC 305 D DG 408 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C DC 5 N4 ? ? ? 1_555 D DG 2 O6 ? ? C DC 305 D DG 408 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C DC 5 O2 ? ? ? 1_555 D DG 2 N2 ? ? C DC 305 D DG 408 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # 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 CTI 201 ? 11 'BINDING SITE FOR RESIDUE CTI A 201' AC2 Software B CA 501 ? 4 'BINDING SITE FOR RESIDUE CA B 501' # 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 11 DC A 5 ? DC A 105 . ? 1_555 ? 2 AC1 11 DG A 6 ? DG A 106 . ? 1_555 ? 3 AC1 11 HOH G . ? HOH A 301 . ? 1_555 ? 4 AC1 11 DC B 1 ? DC B 207 . ? 4_555 ? 5 AC1 11 DG B 2 ? DG B 208 . ? 1_555 ? 6 AC1 11 HOH H . ? HOH B 602 . ? 1_555 ? 7 AC1 11 DC C 5 ? DC C 305 . ? 1_455 ? 8 AC1 11 DG C 6 ? DG C 306 . ? 1_455 ? 9 AC1 11 DC D 1 ? DC D 407 . ? 4_545 ? 10 AC1 11 DG D 2 ? DG D 408 . ? 1_455 ? 11 AC1 11 HOH J . ? HOH D 502 . ? 4_545 ? 12 AC2 4 DC B 5 ? DC B 211 . ? 5_555 ? 13 AC2 4 DG B 6 ? DG B 212 . ? 5_555 ? 14 AC2 4 DG B 6 ? DG B 212 . ? 1_555 ? 15 AC2 4 DG D 6 ? DG D 412 . ? 1_555 ? # _atom_sites.entry_id 4D9Y _atom_sites.fract_transf_matrix[1][1] 0.033079 _atom_sites.fract_transf_matrix[1][2] 0.019098 _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] 0.038196 _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] 0.008386 _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 CA 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 1 101 101 DC DC A . n A 1 2 DG 2 102 102 DG DG A . n A 1 3 DT 3 103 103 DT DT A . n A 1 4 DA 4 104 104 DA DA A . n A 1 5 DC 5 105 105 DC DC A . n A 1 6 DG 6 106 106 DG DG A . n B 1 1 DC 1 207 207 DC DC B . n B 1 2 DG 2 208 208 DG DG B . n B 1 3 DT 3 209 209 DT DT B . n B 1 4 DA 4 210 210 DA DA B . n B 1 5 DC 5 211 211 DC DC B . n B 1 6 DG 6 212 212 DG DG B . n C 1 1 DC 1 301 301 DC DC C . n C 1 2 DG 2 302 302 DG DG C . n C 1 3 DT 3 303 303 DT DT C . n C 1 4 DA 4 304 304 DA DA C . n C 1 5 DC 5 305 305 DC DC C . n C 1 6 DG 6 306 306 DG DG C . n D 1 1 DC 1 407 407 DC DC D . n D 1 2 DG 2 408 408 DG DG D . n D 1 3 DT 3 409 409 DT DT D . n D 1 4 DA 4 410 410 DA DA D . n D 1 5 DC 5 411 411 DC DC D . n D 1 6 DG 6 412 412 DG DG D . 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 E 2 CTI 1 201 606 CTI CTI A . F 3 CA 1 501 501 CA CA B . G 4 HOH 1 301 709 HOH HOH A . H 4 HOH 1 601 708 HOH HOH B . H 4 HOH 2 602 701 HOH HOH B . H 4 HOH 3 603 702 HOH HOH B . I 4 HOH 1 401 703 HOH HOH C . I 4 HOH 2 402 710 HOH HOH C . J 4 HOH 1 501 704 HOH HOH D . J 4 HOH 2 502 705 HOH HOH D . J 4 HOH 3 503 706 HOH HOH D . J 4 HOH 4 504 707 HOH HOH D . J 4 HOH 5 505 711 HOH HOH D . # 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_and_software_defined_assembly PISA dimeric 2 2 author_and_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 A,B,E,F,G,H 2 1 C,D,I,J # 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)' 550 ? 1 MORE -6 ? 1 'SSA (A^2)' 2720 ? 2 'ABSA (A^2)' 370 ? 2 MORE -2 ? 2 'SSA (A^2)' 2640 ? # _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 # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id OP1 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id B _pdbx_struct_conn_angle.ptnr1_label_comp_id DG _pdbx_struct_conn_angle.ptnr1_label_seq_id 6 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id B _pdbx_struct_conn_angle.ptnr1_auth_comp_id DG _pdbx_struct_conn_angle.ptnr1_auth_seq_id 212 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id CA _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id F _pdbx_struct_conn_angle.ptnr2_label_comp_id CA _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id B _pdbx_struct_conn_angle.ptnr2_auth_comp_id CA _pdbx_struct_conn_angle.ptnr2_auth_seq_id 501 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id OP1 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id D _pdbx_struct_conn_angle.ptnr3_label_comp_id DG _pdbx_struct_conn_angle.ptnr3_label_seq_id 6 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id D _pdbx_struct_conn_angle.ptnr3_auth_comp_id DG _pdbx_struct_conn_angle.ptnr3_auth_seq_id 412 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 68.8 _pdbx_struct_conn_angle.value_esd ? # 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 2013-01-23 2 'Structure model' 1 1 2013-03-13 3 'Structure model' 1 2 2017-11-15 4 'Structure model' 1 3 2023-09-13 # _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' 'Refinement description' 2 3 'Structure model' 'Refinement description' 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 3 'Structure model' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_initial_refinement_model 6 4 'Structure model' struct_conn 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.ptnr1_auth_asym_id' 4 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 5 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 6 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 17 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 18 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 19 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_phasing_MR.entry_id 4D9Y _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details ? _pdbx_phasing_MR.R_factor ? _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 3.500 _pdbx_phasing_MR.d_res_low_rotation 26.170 _pdbx_phasing_MR.d_res_high_translation 3.500 _pdbx_phasing_MR.d_res_low_translation 26.170 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 2 MOLREP . ? program 'Alexei Vaguine' alexei@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/molrep.html Fortran_77 ? 3 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de refinement http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 XDS . ? ? ? ? 'data reduction' ? ? ? 6 XDS . ? ? ? ? 'data scaling' ? ? ? # 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 103 ? ? "C1'" A DT 103 ? ? N1 A DT 103 ? ? 110.22 108.30 1.92 0.30 N 2 1 "C1'" A DC 105 ? ? "O4'" A DC 105 ? ? "C4'" A DC 105 ? ? 102.41 110.10 -7.69 1.00 N 3 1 "O4'" A DC 105 ? ? "C1'" A DC 105 ? ? N1 A DC 105 ? ? 110.50 108.30 2.20 0.30 N 4 1 "C1'" B DC 211 ? ? "O4'" B DC 211 ? ? "C4'" B DC 211 ? ? 103.51 110.10 -6.59 1.00 N 5 1 "O4'" B DG 212 ? ? "C1'" B DG 212 ? ? N9 B DG 212 ? ? 110.29 108.30 1.99 0.30 N 6 1 "C1'" C DT 303 ? ? "O4'" C DT 303 ? ? "C4'" C DT 303 ? ? 104.01 110.10 -6.09 1.00 N 7 1 "O4'" C DT 303 ? ? "C1'" C DT 303 ? ? N1 C DT 303 ? ? 110.65 108.30 2.35 0.30 N 8 1 N1 D DC 411 ? ? C2 D DC 411 ? ? O2 D DC 411 ? ? 115.15 118.90 -3.75 0.60 N 9 1 "O4'" D DG 412 ? ? "C1'" D DG 412 ? ? N9 D DG 412 ? ? 103.66 108.00 -4.34 0.70 N # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A DC 101 ? "O5'" ? A DC 1 "O5'" 2 1 Y 1 A DC 101 ? "C5'" ? A DC 1 "C5'" 3 1 Y 1 A DC 101 ? "C4'" ? A DC 1 "C4'" 4 1 Y 1 A DC 101 ? "O4'" ? A DC 1 "O4'" 5 1 Y 1 A DC 101 ? "C3'" ? A DC 1 "C3'" 6 1 Y 1 A DC 101 ? "C2'" ? A DC 1 "C2'" 7 1 Y 1 A DC 101 ? "C1'" ? A DC 1 "C1'" 8 1 Y 1 A DC 101 ? N1 ? A DC 1 N1 9 1 Y 1 A DC 101 ? C2 ? A DC 1 C2 10 1 Y 1 A DC 101 ? O2 ? A DC 1 O2 11 1 Y 1 A DC 101 ? N3 ? A DC 1 N3 12 1 Y 1 A DC 101 ? C4 ? A DC 1 C4 13 1 Y 1 A DC 101 ? N4 ? A DC 1 N4 14 1 Y 1 A DC 101 ? C5 ? A DC 1 C5 15 1 Y 1 A DC 101 ? C6 ? A DC 1 C6 16 1 Y 1 C DC 301 ? "O5'" ? C DC 1 "O5'" 17 1 Y 1 C DC 301 ? "C5'" ? C DC 1 "C5'" 18 1 Y 1 C DC 301 ? "C4'" ? C DC 1 "C4'" 19 1 Y 1 C DC 301 ? "O4'" ? C DC 1 "O4'" 20 1 Y 1 C DC 301 ? "C3'" ? C DC 1 "C3'" 21 1 Y 1 C DC 301 ? "C2'" ? C DC 1 "C2'" 22 1 Y 1 C DC 301 ? "C1'" ? C DC 1 "C1'" 23 1 Y 1 C DC 301 ? N1 ? C DC 1 N1 24 1 Y 1 C DC 301 ? C2 ? C DC 1 C2 25 1 Y 1 C DC 301 ? O2 ? C DC 1 O2 26 1 Y 1 C DC 301 ? N3 ? C DC 1 N3 27 1 Y 1 C DC 301 ? C4 ? C DC 1 C4 28 1 Y 1 C DC 301 ? N4 ? C DC 1 N4 29 1 Y 1 C DC 301 ? C5 ? C DC 1 C5 30 1 Y 1 C DC 301 ? C6 ? C DC 1 C6 # 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 CA CA CA N N 1 CTI C1 C Y N 2 CTI C2 C Y N 3 CTI C3 C Y N 4 CTI C4 C Y N 5 CTI C5 C Y N 6 CTI C6 C Y N 7 CTI C7 C Y N 8 CTI C8 C Y N 9 CTI N9 N Y N 10 CTI C10 C Y N 11 CTI C11 C Y N 12 CTI C12 C Y N 13 CTI C13 C N N 14 CTI C14 C Y N 15 CTI C15 C Y N 16 CTI C16 C Y N 17 CTI C17 C Y N 18 CTI O18 O N N 19 CTI C19 C N N 20 CTI O20 O N N 21 CTI C21 C N N 22 CTI C22 C Y N 23 CTI C23 C Y N 24 CTI O24 O N N 25 CTI C25 C N N 26 CTI O26 O N N 27 CTI H1 H N N 28 CTI H4 H N N 29 CTI H7 H N N 30 CTI H8 H N N 31 CTI H12 H N N 32 CTI H13 H N N 33 CTI H13A H N N 34 CTI H13B H N N 35 CTI H15 H N N 36 CTI H16 H N N 37 CTI H19 H N N 38 CTI H19A H N N 39 CTI H19B H N N 40 CTI H21 H N N 41 CTI H21A H N N 42 CTI H21B H N N 43 CTI H25 H N N 44 CTI H25A H N N 45 DA OP3 O N N 46 DA P P N N 47 DA OP1 O N N 48 DA OP2 O N N 49 DA "O5'" O N N 50 DA "C5'" C N N 51 DA "C4'" C N R 52 DA "O4'" O N N 53 DA "C3'" C N S 54 DA "O3'" O N N 55 DA "C2'" C N N 56 DA "C1'" C N R 57 DA N9 N Y N 58 DA C8 C Y N 59 DA N7 N Y N 60 DA C5 C Y N 61 DA C6 C Y N 62 DA N6 N N N 63 DA N1 N Y N 64 DA C2 C Y N 65 DA N3 N Y N 66 DA C4 C Y N 67 DA HOP3 H N N 68 DA HOP2 H N N 69 DA "H5'" H N N 70 DA "H5''" H N N 71 DA "H4'" H N N 72 DA "H3'" H N N 73 DA "HO3'" H N N 74 DA "H2'" H N N 75 DA "H2''" H N N 76 DA "H1'" H N N 77 DA H8 H N N 78 DA H61 H N N 79 DA H62 H N N 80 DA H2 H N N 81 DC OP3 O N N 82 DC P P N N 83 DC OP1 O N N 84 DC OP2 O N N 85 DC "O5'" O N N 86 DC "C5'" C N N 87 DC "C4'" C N R 88 DC "O4'" O N N 89 DC "C3'" C N S 90 DC "O3'" O N N 91 DC "C2'" C N N 92 DC "C1'" C N R 93 DC N1 N N N 94 DC C2 C N N 95 DC O2 O N N 96 DC N3 N N N 97 DC C4 C N N 98 DC N4 N N N 99 DC C5 C N N 100 DC C6 C N N 101 DC HOP3 H N N 102 DC HOP2 H N N 103 DC "H5'" H N N 104 DC "H5''" H N N 105 DC "H4'" H N N 106 DC "H3'" H N N 107 DC "HO3'" H N N 108 DC "H2'" H N N 109 DC "H2''" H N N 110 DC "H1'" H N N 111 DC H41 H N N 112 DC H42 H N N 113 DC H5 H N N 114 DC H6 H N N 115 DG OP3 O N N 116 DG P P N N 117 DG OP1 O N N 118 DG OP2 O N N 119 DG "O5'" O N N 120 DG "C5'" C N N 121 DG "C4'" C N R 122 DG "O4'" O N N 123 DG "C3'" C N S 124 DG "O3'" O N N 125 DG "C2'" C N N 126 DG "C1'" C N R 127 DG N9 N Y N 128 DG C8 C Y N 129 DG N7 N Y N 130 DG C5 C Y N 131 DG C6 C N N 132 DG O6 O N N 133 DG N1 N N N 134 DG C2 C N N 135 DG N2 N N N 136 DG N3 N N N 137 DG C4 C Y N 138 DG HOP3 H N N 139 DG HOP2 H N N 140 DG "H5'" H N N 141 DG "H5''" H N N 142 DG "H4'" H N N 143 DG "H3'" H N N 144 DG "HO3'" H N N 145 DG "H2'" H N N 146 DG "H2''" H N N 147 DG "H1'" H N N 148 DG H8 H N N 149 DG H1 H N N 150 DG H21 H N N 151 DG H22 H N N 152 DT OP3 O N N 153 DT P P N N 154 DT OP1 O N N 155 DT OP2 O N N 156 DT "O5'" O N N 157 DT "C5'" C N N 158 DT "C4'" C N R 159 DT "O4'" O N N 160 DT "C3'" C N S 161 DT "O3'" O N N 162 DT "C2'" C N N 163 DT "C1'" C N R 164 DT N1 N N N 165 DT C2 C N N 166 DT O2 O N N 167 DT N3 N N N 168 DT C4 C N N 169 DT O4 O N N 170 DT C5 C N N 171 DT C7 C N N 172 DT C6 C N N 173 DT HOP3 H N N 174 DT HOP2 H N N 175 DT "H5'" H N N 176 DT "H5''" H N N 177 DT "H4'" H N N 178 DT "H3'" H N N 179 DT "HO3'" H N N 180 DT "H2'" H N N 181 DT "H2''" H N N 182 DT "H1'" H N N 183 DT H3 H N N 184 DT H71 H N N 185 DT H72 H N N 186 DT H73 H N N 187 DT H6 H N N 188 HOH O O N N 189 HOH H1 H N N 190 HOH H2 H N N 191 # 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 CTI C1 C2 doub Y N 1 CTI C1 C22 sing Y N 2 CTI C2 C3 sing Y N 3 CTI C2 C5 sing Y N 4 CTI C3 C4 doub Y N 5 CTI C3 C8 sing Y N 6 CTI C4 C23 sing Y N 7 CTI C5 C6 doub Y N 8 CTI C5 N9 sing Y N 9 CTI C6 C7 sing Y N 10 CTI C6 C10 sing Y N 11 CTI C7 C8 doub Y N 12 CTI N9 C12 doub Y N 13 CTI N9 C13 sing N N 14 CTI C10 C11 doub Y N 15 CTI C10 C16 sing Y N 16 CTI C11 C12 sing Y N 17 CTI C11 C17 sing Y N 18 CTI C14 C15 sing Y N 19 CTI C14 C17 doub Y N 20 CTI C14 O20 sing N N 21 CTI C15 C16 doub Y N 22 CTI C17 O18 sing N N 23 CTI O18 C19 sing N N 24 CTI O20 C21 sing N N 25 CTI C22 C23 doub Y N 26 CTI C22 O24 sing N N 27 CTI C23 O26 sing N N 28 CTI O24 C25 sing N N 29 CTI C25 O26 sing N N 30 CTI C1 H1 sing N N 31 CTI C4 H4 sing N N 32 CTI C7 H7 sing N N 33 CTI C8 H8 sing N N 34 CTI C12 H12 sing N N 35 CTI C13 H13 sing N N 36 CTI C13 H13A sing N N 37 CTI C13 H13B sing N N 38 CTI C15 H15 sing N N 39 CTI C16 H16 sing N N 40 CTI C19 H19 sing N N 41 CTI C19 H19A sing N N 42 CTI C19 H19B sing N N 43 CTI C21 H21 sing N N 44 CTI C21 H21A sing N N 45 CTI C21 H21B sing N N 46 CTI C25 H25 sing N N 47 CTI C25 H25A sing N N 48 DA OP3 P sing N N 49 DA OP3 HOP3 sing N N 50 DA P OP1 doub N N 51 DA P OP2 sing N N 52 DA P "O5'" sing N N 53 DA OP2 HOP2 sing N N 54 DA "O5'" "C5'" sing N N 55 DA "C5'" "C4'" sing N N 56 DA "C5'" "H5'" sing N N 57 DA "C5'" "H5''" sing N N 58 DA "C4'" "O4'" sing N N 59 DA "C4'" "C3'" sing N N 60 DA "C4'" "H4'" sing N N 61 DA "O4'" "C1'" sing N N 62 DA "C3'" "O3'" sing N N 63 DA "C3'" "C2'" sing N N 64 DA "C3'" "H3'" sing N N 65 DA "O3'" "HO3'" sing N N 66 DA "C2'" "C1'" sing N N 67 DA "C2'" "H2'" sing N N 68 DA "C2'" "H2''" sing N N 69 DA "C1'" N9 sing N N 70 DA "C1'" "H1'" sing N N 71 DA N9 C8 sing Y N 72 DA N9 C4 sing Y N 73 DA C8 N7 doub Y N 74 DA C8 H8 sing N N 75 DA N7 C5 sing Y N 76 DA C5 C6 sing Y N 77 DA C5 C4 doub Y N 78 DA C6 N6 sing N N 79 DA C6 N1 doub Y N 80 DA N6 H61 sing N N 81 DA N6 H62 sing N N 82 DA N1 C2 sing Y N 83 DA C2 N3 doub Y N 84 DA C2 H2 sing N N 85 DA N3 C4 sing Y N 86 DC OP3 P sing N N 87 DC OP3 HOP3 sing N N 88 DC P OP1 doub N N 89 DC P OP2 sing N N 90 DC P "O5'" sing N N 91 DC OP2 HOP2 sing N N 92 DC "O5'" "C5'" sing N N 93 DC "C5'" "C4'" sing N N 94 DC "C5'" "H5'" sing N N 95 DC "C5'" "H5''" sing N N 96 DC "C4'" "O4'" sing N N 97 DC "C4'" "C3'" sing N N 98 DC "C4'" "H4'" sing N N 99 DC "O4'" "C1'" sing N N 100 DC "C3'" "O3'" sing N N 101 DC "C3'" "C2'" sing N N 102 DC "C3'" "H3'" sing N N 103 DC "O3'" "HO3'" sing N N 104 DC "C2'" "C1'" sing N N 105 DC "C2'" "H2'" sing N N 106 DC "C2'" "H2''" sing N N 107 DC "C1'" N1 sing N N 108 DC "C1'" "H1'" sing N N 109 DC N1 C2 sing N N 110 DC N1 C6 sing N N 111 DC C2 O2 doub N N 112 DC C2 N3 sing N N 113 DC N3 C4 doub N N 114 DC C4 N4 sing N N 115 DC C4 C5 sing N N 116 DC N4 H41 sing N N 117 DC N4 H42 sing N N 118 DC C5 C6 doub N N 119 DC C5 H5 sing N N 120 DC C6 H6 sing N N 121 DG OP3 P sing N N 122 DG OP3 HOP3 sing N N 123 DG P OP1 doub N N 124 DG P OP2 sing N N 125 DG P "O5'" sing N N 126 DG OP2 HOP2 sing N N 127 DG "O5'" "C5'" sing N N 128 DG "C5'" "C4'" sing N N 129 DG "C5'" "H5'" sing N N 130 DG "C5'" "H5''" sing N N 131 DG "C4'" "O4'" sing N N 132 DG "C4'" "C3'" sing N N 133 DG "C4'" "H4'" sing N N 134 DG "O4'" "C1'" sing N N 135 DG "C3'" "O3'" sing N N 136 DG "C3'" "C2'" sing N N 137 DG "C3'" "H3'" sing N N 138 DG "O3'" "HO3'" sing N N 139 DG "C2'" "C1'" sing N N 140 DG "C2'" "H2'" sing N N 141 DG "C2'" "H2''" sing N N 142 DG "C1'" N9 sing N N 143 DG "C1'" "H1'" sing N N 144 DG N9 C8 sing Y N 145 DG N9 C4 sing Y N 146 DG C8 N7 doub Y N 147 DG C8 H8 sing N N 148 DG N7 C5 sing Y N 149 DG C5 C6 sing N N 150 DG C5 C4 doub Y N 151 DG C6 O6 doub N N 152 DG C6 N1 sing N N 153 DG N1 C2 sing N N 154 DG N1 H1 sing N N 155 DG C2 N2 sing N N 156 DG C2 N3 doub N N 157 DG N2 H21 sing N N 158 DG N2 H22 sing N N 159 DG N3 C4 sing N N 160 DT OP3 P sing N N 161 DT OP3 HOP3 sing N N 162 DT P OP1 doub N N 163 DT P OP2 sing N N 164 DT P "O5'" sing N N 165 DT OP2 HOP2 sing N N 166 DT "O5'" "C5'" sing N N 167 DT "C5'" "C4'" sing N N 168 DT "C5'" "H5'" sing N N 169 DT "C5'" "H5''" sing N N 170 DT "C4'" "O4'" sing N N 171 DT "C4'" "C3'" sing N N 172 DT "C4'" "H4'" sing N N 173 DT "O4'" "C1'" sing N N 174 DT "C3'" "O3'" sing N N 175 DT "C3'" "C2'" sing N N 176 DT "C3'" "H3'" sing N N 177 DT "O3'" "HO3'" sing N N 178 DT "C2'" "C1'" sing N N 179 DT "C2'" "H2'" sing N N 180 DT "C2'" "H2''" sing N N 181 DT "C1'" N1 sing N N 182 DT "C1'" "H1'" sing N N 183 DT N1 C2 sing N N 184 DT N1 C6 sing N N 185 DT C2 O2 doub N N 186 DT C2 N3 sing N N 187 DT N3 C4 sing N N 188 DT N3 H3 sing N N 189 DT C4 O4 doub N N 190 DT C4 C5 sing N N 191 DT C5 C7 sing N N 192 DT C5 C6 doub N N 193 DT C7 H71 sing N N 194 DT C7 H72 sing N N 195 DT C7 H73 sing N N 196 DT C6 H6 sing N N 197 HOH O H1 sing N N 198 HOH O H2 sing N N 199 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4D9Y 'double helix' 4D9Y '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 B DG 2 1_555 A DC 5 1_555 -0.289 -0.286 0.297 -19.257 -5.579 -6.882 1 B_DG208:DC105_A B 208 ? A 105 ? 19 1 1 B DT 3 1_555 A DA 4 1_555 0.750 0.224 -0.493 4.724 -13.910 -4.004 2 B_DT209:DA104_A B 209 ? A 104 ? 20 1 1 B DA 4 1_555 A DT 3 1_555 1.153 -0.139 0.882 -6.397 -4.631 7.029 3 B_DA210:DT103_A B 210 ? A 103 ? 20 1 1 B DC 5 1_555 A DG 2 1_555 0.898 -0.194 0.324 1.049 7.937 -0.752 4 B_DC211:DG102_A B 211 ? A 102 ? 19 1 1 C DG 2 1_555 D DC 5 1_555 -0.344 0.041 -0.163 -5.707 -3.501 10.803 5 C_DG302:DC411_D C 302 ? D 411 ? 19 1 1 C DT 3 1_555 D DA 4 1_555 -0.098 -0.605 1.254 -8.841 -7.406 -11.888 6 C_DT303:DA410_D C 303 ? D 410 ? 20 1 1 C DA 4 1_555 D DT 3 1_555 -0.047 0.428 0.330 6.144 -9.485 -0.577 7 C_DA304:DT409_D C 304 ? D 409 ? ? ? 1 C DC 5 1_555 D DG 2 1_555 0.375 -0.444 0.433 11.921 -13.514 -3.863 8 C_DC305:DG408_D C 305 ? D 408 ? 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 B DG 2 1_555 A DC 5 1_555 B DT 3 1_555 A DA 4 1_555 -0.757 -0.322 2.698 8.949 4.136 31.113 -1.140 2.576 2.336 7.479 -16.183 32.601 1 BB_DG208DT209:DA104DC105_AA B 208 ? A 105 ? B 209 ? A 104 ? 1 B DT 3 1_555 A DA 4 1_555 B DA 4 1_555 A DT 3 1_555 0.123 -0.623 3.490 -11.817 3.820 41.319 -1.247 -1.399 3.270 5.272 16.308 43.067 2 BB_DT209DA210:DT103DA104_AA B 209 ? A 104 ? B 210 ? A 103 ? 1 B DA 4 1_555 A DT 3 1_555 B DC 5 1_555 A DG 2 1_555 -0.037 -0.519 3.173 5.025 -1.005 24.188 -0.914 1.573 3.119 -2.364 -11.823 24.717 3 BB_DA210DC211:DG102DT103_AA B 210 ? A 103 ? B 211 ? A 102 ? 1 B DC 5 1_555 A DG 2 1_555 C DG 2 1_555 D DC 5 1_555 0.400 1.098 3.325 7.108 5.801 -69.323 -1.167 0.603 3.188 -5.078 6.221 -69.852 4 BC_DC211DG302:DC411DG102_DA B 211 ? A 102 ? C 302 ? D 411 ? 1 C DG 2 1_555 D DC 5 1_555 C DT 3 1_555 D DA 4 1_555 -1.040 -0.405 3.599 -13.277 1.387 26.166 -1.153 -1.315 3.662 2.841 27.191 29.322 5 CC_DG302DT303:DA410DC411_DD C 302 ? D 411 ? C 303 ? D 410 ? 1 C DT 3 1_555 D DA 4 1_555 C DA 4 1_555 D DT 3 1_555 0.367 -0.691 2.864 9.793 -7.111 38.118 -0.266 0.490 2.944 -10.568 -14.554 39.925 6 CC_DT303DA304:DT409DA410_DD C 303 ? D 410 ? C 304 ? D 409 ? 1 C DA 4 1_555 D DT 3 1_555 C DC 5 1_555 D DG 2 1_555 0.808 -0.811 3.113 -2.680 8.661 34.569 -2.468 -1.672 2.768 14.273 4.416 35.703 7 CC_DA304DC305:DG408DT409_DD C 304 ? D 409 ? C 305 ? D 408 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium' CTI 3 'CALCIUM ION' CA 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 3NP6 _pdbx_initial_refinement_model.details 'PDB ENTRY 3NP6' #