data_3NP6 # _entry.id 3NP6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3NP6 pdb_00003np6 10.2210/pdb3np6/pdb NDB NA0614 ? ? RCSB RCSB060105 ? ? WWPDB D_1000060105 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3NX5 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3NP6 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2010-06-28 _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 ;X-Ray diffraction analyses of the natural isoquinoline alkaloids Berberine and Sanguinarine complexed with double helix DNA d(CGTACG) ; _citation.journal_abbrev 'Chem.Commun.(Camb.)' _citation.journal_volume 47 _citation.page_first 4917 _citation.page_last 4919 _citation.year 2011 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1359-7345 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21431128 _citation.pdbx_database_id_DOI 10.1039/c1cc10971e # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ferraroni, M.' 1 ? primary 'Bazzicalupi, C.' 2 ? primary 'Bilia, A.R.' 3 ? primary 'Gratteri, P.' 4 ? # _cell.length_a 30.370 _cell.length_b 30.370 _cell.length_c 118.260 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3NP6 _cell.pdbx_unique_axis ? _cell.Z_PDB 24 _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.space_group_name_H-M 'P 32 2 1' _symmetry.entry_id 3NP6 _symmetry.Int_Tables_number 154 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*CP*GP*TP*AP*CP*G)-3'" 1809.217 4 ? ? ? ? 2 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 3 non-polymer syn BERBERINE 336.361 1 ? ? ? ? 4 water nat water 18.015 1 ? ? ? ? # _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 3NP6 _struct_ref.pdbx_db_accession 3NP6 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3NP6 A 1 ? 6 ? 3NP6 1 ? 6 ? 1 6 2 1 3NP6 B 1 ? 6 ? 3NP6 7 ? 12 ? 7 12 3 1 3NP6 C 1 ? 6 ? 3NP6 1 ? 6 ? 1 6 4 1 3NP6 D 1 ? 6 ? 3NP6 7 ? 12 ? 7 12 # 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 BER non-polymer . BERBERINE ? 'C20 H18 N O4 1' 336.361 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 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.crystals_number 1 _exptl.entry_id 3NP6 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 43.46 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _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.pH 6.5 _exptl_crystal_grow.temp 296 _exptl_crystal_grow.pdbx_details 'MPD, MgCl2, NaCl, pH 6.5, vapor diffusion, temperature 296K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'OXFORD ONYX CCD' _diffrn_detector.pdbx_collection_date 2010-01-22 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.542 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'SEALED TUBE' _diffrn_source.type 'OXFORD DIFFRACTION ENHANCE ULTRA' _diffrn_source.pdbx_wavelength_list 1.542 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id 3NP6 _reflns.d_resolution_high 2.300 _reflns.number_obs 3159 _reflns.pdbx_Rmerge_I_obs 0.076 _reflns.pdbx_netI_over_sigmaI 29.040 _reflns.percent_possible_obs 100.000 _reflns.B_iso_Wilson_estimate 43.450 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 39.4200 _reflns.number_all ? _reflns.pdbx_Rsym_value 0.076 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.300 2.400 7573 ? 653 ? 0.558 4.8 ? ? ? ? ? 654 ? ? 0.325 ? ? 99.800 0.584 ? 1 1 2.400 2.600 17213 ? 1019 ? 0.384 9.1 ? ? ? ? ? 1019 ? ? 0.153 ? ? 100.000 0.396 ? 2 1 2.600 2.800 14237 ? 738 ? 0.220 14.8 ? ? ? ? ? 738 ? ? 0.085 ? ? 100.000 0.226 ? 3 1 2.800 2.900 6047 ? 291 ? 0.177 18.7 ? ? ? ? ? 291 ? ? 0.060 ? ? 100.000 0.181 ? 4 1 2.900 3.000 5761 ? 273 ? 0.139 23.9 ? ? ? ? ? 273 ? ? 0.049 ? ? 100.000 0.142 ? 5 1 3.000 3.120 5891 ? 277 ? 0.104 29.6 ? ? ? ? ? 277 ? ? 0.038 ? ? 100.000 0.106 ? 6 1 3.120 3.270 6092 ? 278 ? 0.065 41.4 ? ? ? ? ? 278 ? ? 0.020 ? ? 100.000 0.067 ? 7 1 3.270 3.440 5881 ? 272 ? 0.059 46.1 ? ? ? ? ? 272 ? ? 0.018 ? ? 100.000 0.061 ? 8 1 3.440 3.650 5846 ? 263 ? 0.054 51.3 ? ? ? ? ? 263 ? ? 0.015 ? ? 100.000 0.056 ? 9 1 3.650 3.940 6152 ? 277 ? 0.060 52.3 ? ? ? ? ? 277 ? ? 0.017 ? ? 100.000 0.061 ? 10 1 3.940 4.330 6018 ? 285 ? 0.056 55.2 ? ? ? ? ? 285 ? ? 0.015 ? ? 100.000 0.057 ? 11 1 4.330 4.960 5571 ? 259 ? 0.056 55.4 ? ? ? ? ? 259 ? ? 0.017 ? ? 100.000 0.058 ? 12 1 4.960 6.250 5776 ? 272 ? 0.057 56.4 ? ? ? ? ? 272 ? ? 0.015 ? ? 100.000 0.058 ? 13 1 6.250 10.000 4592 ? 211 ? 0.049 61.8 ? ? ? ? ? 211 ? ? 0.013 ? ? 100.000 0.050 ? 14 1 10.000 15.000 863 ? 38 ? 0.041 64.6 ? ? ? ? ? 38 ? ? 0.010 ? ? 100.000 0.041 ? 15 1 15.000 39.420 351 ? 19 ? 0.030 61.0 ? ? ? ? ? 19 ? ? 0.010 ? ? 100.000 0.031 ? 16 1 # _refine.entry_id 3NP6 _refine.ls_d_res_high 2.3000 _refine.ls_d_res_low 39.4200 _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.9400 _refine.ls_number_reflns_obs 3153 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2387 _refine.ls_R_factor_R_work 0.2361 _refine.ls_wR_factor_R_work 0.2204 _refine.ls_R_factor_R_free 0.3014 _refine.ls_wR_factor_R_free 0.2752 _refine.ls_percent_reflns_R_free 4.4000 _refine.ls_number_reflns_R_free 139 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 18.1113 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _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.correlation_coeff_Fo_to_Fc 0.9380 _refine.correlation_coeff_Fo_to_Fc_free 0.8820 _refine.overall_SU_R_Cruickshank_DPI 0.0769 _refine.overall_SU_R_free 0.0594 _refine.pdbx_overall_ESU_R_Free 0.0590 _refine.overall_SU_ML 0.2120 _refine.overall_SU_B ? _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 'PDB ENTRY 1XCS' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.7005 _refine.B_iso_max 36.440 _refine.B_iso_min 2.000 _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 450 _refine_hist.pdbx_number_atoms_ligand 26 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 477 _refine_hist.d_res_high 2.3000 _refine_hist.d_res_low 39.4200 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 531 0.007 0.021 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 813 1.842 3.000 ? 'X-RAY DIFFRACTION' ? ;CHIRAL-CENTER RESTRAINTS (A'*3) ; 87 0.091 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 258 0.007 0.020 ? 'X-RAY DIFFRACTION' ? ;MAIN-CHAIN BOND REFINED ATOMS (A'*2) ; 3 0.189 1.500 ? 'X-RAY DIFFRACTION' ? ;MAIN-CHAIN ANGLE REFINED ATOMS (A'*2) ; 4 0.358 2.000 ? 'X-RAY DIFFRACTION' ? ;SIDE-CHAIN BOND REFINED ATOMS (A'*2) ; 528 1.454 3.000 ? 'X-RAY DIFFRACTION' ? ;SIDE-CHAIN ANGLE REFINED ATOMS (A'*2) ; 809 2.547 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.3000 _refine_ls_shell.d_res_low 2.3600 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.5400 _refine_ls_shell.number_reflns_R_work 212 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.4410 _refine_ls_shell.R_factor_R_free 0.3850 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 6 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 218 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 3NP6 _struct.title 'The crystal structure of Berberine bound to DNA d(CGTACG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3NP6 _struct_keywords.text 'DRUG-DNA COMPLEX, DOUBLE HELIX, B-DNA, 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 ? # _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 ? ? E CA . CA ? ? ? 1_555 B DG 6 OP1 ? ? B CA 1 B DG 12 1_555 ? ? ? ? ? ? ? 2.162 ? ? metalc2 metalc ? ? E CA . CA ? ? ? 1_555 D DG 6 OP1 ? ? B CA 1 D DG 12 1_555 ? ? ? ? ? ? ? 2.464 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N2 ? ? ? 1_555 D DG 6 N3 ? ? A DG 2 D DG 12 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog5 hydrog ? ? A DG 2 N3 ? ? ? 1_555 D DG 6 N2 ? ? A DG 2 D DG 12 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog6 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B DG 6 N2 ? ? ? 1_555 C DG 2 N3 ? ? B DG 12 C DG 2 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog14 hydrog ? ? B DG 6 N3 ? ? ? 1_555 C DG 2 N2 ? ? B DG 12 C DG 2 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog15 hydrog ? ? C DG 2 N1 ? ? ? 1_555 D DC 5 N3 ? ? C DG 2 D DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? C DG 2 N2 ? ? ? 1_555 D DC 5 O2 ? ? C DG 2 D DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? C DG 2 O6 ? ? ? 1_555 D DC 5 N4 ? ? C DG 2 D DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? C DT 3 N3 ? ? ? 1_555 D DA 4 N1 ? ? C DT 3 D DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? C DT 3 O4 ? ? ? 1_555 D DA 4 N6 ? ? C DT 3 D DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? C DA 4 N1 ? ? ? 1_555 D DT 3 N3 ? ? C DA 4 D DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C DA 4 N6 ? ? ? 1_555 D DT 3 O4 ? ? C DA 4 D DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C DC 5 N3 ? ? ? 1_555 D DG 2 N1 ? ? C DC 5 D DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C DC 5 N4 ? ? ? 1_555 D DG 2 O6 ? ? C DC 5 D DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C DC 5 O2 ? ? ? 1_555 D DG 2 N2 ? ? C DC 5 D DG 8 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 C BER 7 ? 8 'BINDING SITE FOR RESIDUE BER C 7' AC2 Software B CA 1 ? 3 'BINDING SITE FOR RESIDUE CA B 1' 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 DC A 5 ? DC A 5 . ? 1_665 ? 2 AC1 8 DG A 6 ? DG A 6 . ? 1_665 ? 3 AC1 8 DC B 1 ? DC B 7 . ? 5_665 ? 4 AC1 8 DG B 2 ? DG B 8 . ? 1_665 ? 5 AC1 8 DC C 5 ? DC C 5 . ? 1_555 ? 6 AC1 8 DG C 6 ? DG C 6 . ? 1_555 ? 7 AC1 8 DC D 1 ? DC D 7 . ? 5_675 ? 8 AC1 8 DG D 2 ? DG D 8 . ? 1_555 ? 9 AC2 3 DG B 6 ? DG B 12 . ? 1_555 ? 10 AC2 3 DG D 6 ? DG D 12 . ? 1_555 ? 11 AC2 3 DG D 6 ? DG D 12 . ? 4_555 ? # _atom_sites.entry_id 3NP6 _atom_sites.fract_transf_matrix[1][1] 0.032927 _atom_sites.fract_transf_matrix[1][2] 0.019011 _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] 0.038021 _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] 0.008456 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # 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 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n B 1 1 DC 1 7 7 DC DC B . n B 1 2 DG 2 8 8 DG DG B . n B 1 3 DT 3 9 9 DT DT B . n B 1 4 DA 4 10 10 DA DA B . n B 1 5 DC 5 11 11 DC DC B . n B 1 6 DG 6 12 12 DG DG B . n C 1 1 DC 1 1 1 DC DC C . n C 1 2 DG 2 2 2 DG DG C . n C 1 3 DT 3 3 3 DT DT C . n C 1 4 DA 4 4 4 DA DA C . n C 1 5 DC 5 5 5 DC DC C . n C 1 6 DG 6 6 6 DG DG C . n D 1 1 DC 1 7 7 DC DC D . n D 1 2 DG 2 8 8 DG DG D . n D 1 3 DT 3 9 9 DT DT D . n D 1 4 DA 4 10 10 DA DA D . n D 1 5 DC 5 11 11 DC DC D . n D 1 6 DG 6 12 12 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 CA 1 1 1 CA CA B . F 3 BER 1 7 1 BER BER C . G 4 HOH 1 1 1 HOH HOH D . # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # 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 2 1 C,D,F,G # 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)' 360 ? 1 MORE -2 ? 1 'SSA (A^2)' 2700 ? 2 'ABSA (A^2)' 360 ? 2 MORE -2 ? 2 'SSA (A^2)' 2700 ? # _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 12 _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 E _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 1 _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 12 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 79.6 _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 2011-05-04 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-11-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 4 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 5 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 6 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 7 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 11 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 12 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 15 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 17 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 18 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 19 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_phasing_MR.entry_id 3NP6 _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 39.420 _pdbx_phasing_MR.d_res_high_translation 3.500 _pdbx_phasing_MR.d_res_low_translation 39.420 _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 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html 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 CrysalisPro . ? ? ? ? 'data collection' ? ? ? 6 XDS . ? ? ? ? 'data reduction' ? ? ? # 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 DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 110.91 108.30 2.61 0.30 N 2 1 C6 B DA 10 ? ? N1 B DA 10 ? ? C2 B DA 10 ? ? 114.17 118.60 -4.43 0.60 N 3 1 C8 B DA 10 ? ? N9 B DA 10 ? ? C4 B DA 10 ? ? 103.33 105.80 -2.47 0.40 N 4 1 N1 B DC 11 ? ? C2 B DC 11 ? ? O2 B DC 11 ? ? 122.87 118.90 3.97 0.60 N 5 1 "O4'" C DC 5 ? ? "C1'" C DC 5 ? ? N1 C DC 5 ? ? 112.49 108.30 4.19 0.30 N 6 1 "O4'" D DC 11 ? ? "C1'" D DC 11 ? ? N1 D DC 11 ? ? 111.08 108.30 2.78 0.30 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 1 ? "O5'" ? A DC 1 "O5'" 2 1 Y 1 A DC 1 ? "C5'" ? A DC 1 "C5'" 3 1 Y 1 A DC 1 ? "C4'" ? A DC 1 "C4'" 4 1 Y 1 A DC 1 ? "O4'" ? A DC 1 "O4'" 5 1 Y 1 A DC 1 ? "C3'" ? A DC 1 "C3'" 6 1 Y 1 A DC 1 ? "C2'" ? A DC 1 "C2'" 7 1 Y 1 A DC 1 ? "C1'" ? A DC 1 "C1'" 8 1 Y 1 A DC 1 ? N1 ? A DC 1 N1 9 1 Y 1 A DC 1 ? C2 ? A DC 1 C2 10 1 Y 1 A DC 1 ? O2 ? A DC 1 O2 11 1 Y 1 A DC 1 ? N3 ? A DC 1 N3 12 1 Y 1 A DC 1 ? C4 ? A DC 1 C4 13 1 Y 1 A DC 1 ? N4 ? A DC 1 N4 14 1 Y 1 A DC 1 ? C5 ? A DC 1 C5 15 1 Y 1 A DC 1 ? C6 ? A DC 1 C6 16 1 Y 1 C DC 1 ? "O5'" ? C DC 1 "O5'" 17 1 Y 1 C DC 1 ? "C5'" ? C DC 1 "C5'" 18 1 Y 1 C DC 1 ? "C4'" ? C DC 1 "C4'" 19 1 Y 1 C DC 1 ? "O4'" ? C DC 1 "O4'" 20 1 Y 1 C DC 1 ? "C3'" ? C DC 1 "C3'" 21 1 Y 1 C DC 1 ? "C2'" ? C DC 1 "C2'" 22 1 Y 1 C DC 1 ? "C1'" ? C DC 1 "C1'" 23 1 Y 1 C DC 1 ? N1 ? C DC 1 N1 24 1 Y 1 C DC 1 ? C2 ? C DC 1 C2 25 1 Y 1 C DC 1 ? O2 ? C DC 1 O2 26 1 Y 1 C DC 1 ? N3 ? C DC 1 N3 27 1 Y 1 C DC 1 ? C4 ? C DC 1 C4 28 1 Y 1 C DC 1 ? N4 ? C DC 1 N4 29 1 Y 1 C DC 1 ? C5 ? C DC 1 C5 30 1 Y 1 C DC 1 ? 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 BER C1 C Y N 1 BER C2 C Y N 2 BER N1 N Y N 3 BER C3 C Y N 4 BER C4 C Y N 5 BER C5 C Y N 6 BER C6 C Y N 7 BER C7 C N N 8 BER C8 C Y N 9 BER C9 C Y N 10 BER C10 C N N 11 BER C11 C Y N 12 BER C12 C Y N 13 BER C13 C Y N 14 BER C14 C Y N 15 BER O1 O N N 16 BER C15 C Y N 17 BER C16 C Y N 18 BER O2 O N N 19 BER C17 C N N 20 BER C18 C Y N 21 BER O3 O N N 22 BER O4 O N N 23 BER C19 C N N 24 BER C20 C N N 25 BER H31 H N N 26 BER H51 H N N 27 BER H61 H N N 28 BER H71 H N N 29 BER H72 H N N 30 BER H91 H N N 31 BER H101 H N N 32 BER H102 H N N 33 BER H131 H N N 34 BER H161 H N N 35 BER H171 H N N 36 BER H172 H N N 37 BER H191 H N N 38 BER H192 H N N 39 BER H193 H N N 40 BER H201 H N N 41 BER H202 H N N 42 BER H203 H N N 43 CA CA CA N N 44 DA OP3 O N N 45 DA P P N N 46 DA OP1 O N N 47 DA OP2 O N N 48 DA "O5'" O N N 49 DA "C5'" C N N 50 DA "C4'" C N R 51 DA "O4'" O N N 52 DA "C3'" C N S 53 DA "O3'" O N N 54 DA "C2'" C N N 55 DA "C1'" C N R 56 DA N9 N Y N 57 DA C8 C Y N 58 DA N7 N Y N 59 DA C5 C Y N 60 DA C6 C Y N 61 DA N6 N N N 62 DA N1 N Y N 63 DA C2 C Y N 64 DA N3 N Y N 65 DA C4 C Y N 66 DA HOP3 H N N 67 DA HOP2 H N N 68 DA "H5'" H N N 69 DA "H5''" H N N 70 DA "H4'" H N N 71 DA "H3'" H N N 72 DA "HO3'" H N N 73 DA "H2'" H N N 74 DA "H2''" H N N 75 DA "H1'" H N N 76 DA H8 H N N 77 DA H61 H N N 78 DA H62 H N N 79 DA H2 H N N 80 DC OP3 O N N 81 DC P P N N 82 DC OP1 O N N 83 DC OP2 O N N 84 DC "O5'" O N N 85 DC "C5'" C N N 86 DC "C4'" C N R 87 DC "O4'" O N N 88 DC "C3'" C N S 89 DC "O3'" O N N 90 DC "C2'" C N N 91 DC "C1'" C N R 92 DC N1 N N N 93 DC C2 C N N 94 DC O2 O N N 95 DC N3 N N N 96 DC C4 C N N 97 DC N4 N N N 98 DC C5 C N N 99 DC C6 C N N 100 DC HOP3 H N N 101 DC HOP2 H N N 102 DC "H5'" H N N 103 DC "H5''" H N N 104 DC "H4'" H N N 105 DC "H3'" H N N 106 DC "HO3'" H N N 107 DC "H2'" H N N 108 DC "H2''" H N N 109 DC "H1'" H N N 110 DC H41 H N N 111 DC H42 H N N 112 DC H5 H N N 113 DC H6 H N N 114 DG OP3 O N N 115 DG P P N N 116 DG OP1 O N N 117 DG OP2 O N N 118 DG "O5'" O N N 119 DG "C5'" C N N 120 DG "C4'" C N R 121 DG "O4'" O N N 122 DG "C3'" C N S 123 DG "O3'" O N N 124 DG "C2'" C N N 125 DG "C1'" C N R 126 DG N9 N Y N 127 DG C8 C Y N 128 DG N7 N Y N 129 DG C5 C Y N 130 DG C6 C N N 131 DG O6 O N N 132 DG N1 N N N 133 DG C2 C N N 134 DG N2 N N N 135 DG N3 N N N 136 DG C4 C Y N 137 DG HOP3 H N N 138 DG HOP2 H N N 139 DG "H5'" H N N 140 DG "H5''" H N N 141 DG "H4'" H N N 142 DG "H3'" H N N 143 DG "HO3'" H N N 144 DG "H2'" H N N 145 DG "H2''" H N N 146 DG "H1'" H N N 147 DG H8 H N N 148 DG H1 H N N 149 DG H21 H N N 150 DG H22 H N N 151 DT OP3 O N N 152 DT P P N N 153 DT OP1 O N N 154 DT OP2 O N N 155 DT "O5'" O N N 156 DT "C5'" C N N 157 DT "C4'" C N R 158 DT "O4'" O N N 159 DT "C3'" C N S 160 DT "O3'" O N N 161 DT "C2'" C N N 162 DT "C1'" C N R 163 DT N1 N N N 164 DT C2 C N N 165 DT O2 O N N 166 DT N3 N N N 167 DT C4 C N N 168 DT O4 O N N 169 DT C5 C N N 170 DT C7 C N N 171 DT C6 C N N 172 DT HOP3 H N N 173 DT HOP2 H N N 174 DT "H5'" H N N 175 DT "H5''" H N N 176 DT "H4'" H N N 177 DT "H3'" H N N 178 DT "HO3'" H N N 179 DT "H2'" H N N 180 DT "H2''" H N N 181 DT "H1'" H N N 182 DT H3 H N N 183 DT H71 H N N 184 DT H72 H N N 185 DT H73 H N N 186 DT H6 H N N 187 HOH O O N N 188 HOH H1 H N N 189 HOH H2 H N N 190 # 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 BER C1 C2 sing Y N 1 BER C1 N1 doub Y N 2 BER C1 C3 sing Y N 3 BER C2 C4 doub Y N 4 BER C2 C5 sing Y N 5 BER N1 C6 sing Y N 6 BER N1 C7 sing N N 7 BER C3 C8 doub Y N 8 BER C3 H31 sing N N 9 BER C4 C9 sing Y N 10 BER C4 C10 sing N N 11 BER C5 C11 doub Y N 12 BER C5 H51 sing N N 13 BER C6 C12 doub Y N 14 BER C6 H61 sing N N 15 BER C7 C10 sing N N 16 BER C7 H71 sing N N 17 BER C7 H72 sing N N 18 BER C8 C12 sing Y N 19 BER C8 C13 sing Y N 20 BER C9 C14 doub Y N 21 BER C9 H91 sing N N 22 BER C10 H101 sing N N 23 BER C10 H102 sing N N 24 BER C11 C14 sing Y N 25 BER C11 O1 sing N N 26 BER C12 C15 sing Y N 27 BER C13 C16 doub Y N 28 BER C13 H131 sing N N 29 BER C14 O2 sing N N 30 BER O1 C17 sing N N 31 BER C15 C18 doub Y N 32 BER C15 O3 sing N N 33 BER C16 C18 sing Y N 34 BER C16 H161 sing N N 35 BER O2 C17 sing N N 36 BER C17 H171 sing N N 37 BER C17 H172 sing N N 38 BER C18 O4 sing N N 39 BER O3 C19 sing N N 40 BER O4 C20 sing N N 41 BER C19 H191 sing N N 42 BER C19 H192 sing N N 43 BER C19 H193 sing N N 44 BER C20 H201 sing N N 45 BER C20 H202 sing N N 46 BER C20 H203 sing N N 47 DA OP3 P sing N N 48 DA OP3 HOP3 sing N N 49 DA P OP1 doub N N 50 DA P OP2 sing N N 51 DA P "O5'" sing N N 52 DA OP2 HOP2 sing N N 53 DA "O5'" "C5'" sing N N 54 DA "C5'" "C4'" sing N N 55 DA "C5'" "H5'" sing N N 56 DA "C5'" "H5''" sing N N 57 DA "C4'" "O4'" sing N N 58 DA "C4'" "C3'" sing N N 59 DA "C4'" "H4'" sing N N 60 DA "O4'" "C1'" sing N N 61 DA "C3'" "O3'" sing N N 62 DA "C3'" "C2'" sing N N 63 DA "C3'" "H3'" sing N N 64 DA "O3'" "HO3'" sing N N 65 DA "C2'" "C1'" sing N N 66 DA "C2'" "H2'" sing N N 67 DA "C2'" "H2''" sing N N 68 DA "C1'" N9 sing N N 69 DA "C1'" "H1'" sing N N 70 DA N9 C8 sing Y N 71 DA N9 C4 sing Y N 72 DA C8 N7 doub Y N 73 DA C8 H8 sing N N 74 DA N7 C5 sing Y N 75 DA C5 C6 sing Y N 76 DA C5 C4 doub Y N 77 DA C6 N6 sing N N 78 DA C6 N1 doub Y N 79 DA N6 H61 sing N N 80 DA N6 H62 sing N N 81 DA N1 C2 sing Y N 82 DA C2 N3 doub Y N 83 DA C2 H2 sing N N 84 DA N3 C4 sing Y N 85 DC OP3 P sing N N 86 DC OP3 HOP3 sing N N 87 DC P OP1 doub N N 88 DC P OP2 sing N N 89 DC P "O5'" sing N N 90 DC OP2 HOP2 sing N N 91 DC "O5'" "C5'" sing N N 92 DC "C5'" "C4'" sing N N 93 DC "C5'" "H5'" sing N N 94 DC "C5'" "H5''" sing N N 95 DC "C4'" "O4'" sing N N 96 DC "C4'" "C3'" sing N N 97 DC "C4'" "H4'" sing N N 98 DC "O4'" "C1'" sing N N 99 DC "C3'" "O3'" sing N N 100 DC "C3'" "C2'" sing N N 101 DC "C3'" "H3'" sing N N 102 DC "O3'" "HO3'" sing N N 103 DC "C2'" "C1'" sing N N 104 DC "C2'" "H2'" sing N N 105 DC "C2'" "H2''" sing N N 106 DC "C1'" N1 sing N N 107 DC "C1'" "H1'" sing N N 108 DC N1 C2 sing N N 109 DC N1 C6 sing N N 110 DC C2 O2 doub N N 111 DC C2 N3 sing N N 112 DC N3 C4 doub N N 113 DC C4 N4 sing N N 114 DC C4 C5 sing N N 115 DC N4 H41 sing N N 116 DC N4 H42 sing N N 117 DC C5 C6 doub N N 118 DC C5 H5 sing N N 119 DC C6 H6 sing N N 120 DG OP3 P sing N N 121 DG OP3 HOP3 sing N N 122 DG P OP1 doub N N 123 DG P OP2 sing N N 124 DG P "O5'" sing N N 125 DG OP2 HOP2 sing N N 126 DG "O5'" "C5'" sing N N 127 DG "C5'" "C4'" sing N N 128 DG "C5'" "H5'" sing N N 129 DG "C5'" "H5''" sing N N 130 DG "C4'" "O4'" sing N N 131 DG "C4'" "C3'" sing N N 132 DG "C4'" "H4'" sing N N 133 DG "O4'" "C1'" sing N N 134 DG "C3'" "O3'" sing N N 135 DG "C3'" "C2'" sing N N 136 DG "C3'" "H3'" sing N N 137 DG "O3'" "HO3'" sing N N 138 DG "C2'" "C1'" sing N N 139 DG "C2'" "H2'" sing N N 140 DG "C2'" "H2''" sing N N 141 DG "C1'" N9 sing N N 142 DG "C1'" "H1'" sing N N 143 DG N9 C8 sing Y N 144 DG N9 C4 sing Y N 145 DG C8 N7 doub Y N 146 DG C8 H8 sing N N 147 DG N7 C5 sing Y N 148 DG C5 C6 sing N N 149 DG C5 C4 doub Y N 150 DG C6 O6 doub N N 151 DG C6 N1 sing N N 152 DG N1 C2 sing N N 153 DG N1 H1 sing N N 154 DG C2 N2 sing N N 155 DG C2 N3 doub N N 156 DG N2 H21 sing N N 157 DG N2 H22 sing N N 158 DG N3 C4 sing N N 159 DT OP3 P sing N N 160 DT OP3 HOP3 sing N N 161 DT P OP1 doub N N 162 DT P OP2 sing N N 163 DT P "O5'" sing N N 164 DT OP2 HOP2 sing N N 165 DT "O5'" "C5'" sing N N 166 DT "C5'" "C4'" sing N N 167 DT "C5'" "H5'" sing N N 168 DT "C5'" "H5''" sing N N 169 DT "C4'" "O4'" sing N N 170 DT "C4'" "C3'" sing N N 171 DT "C4'" "H4'" sing N N 172 DT "O4'" "C1'" sing N N 173 DT "C3'" "O3'" sing N N 174 DT "C3'" "C2'" sing N N 175 DT "C3'" "H3'" sing N N 176 DT "O3'" "HO3'" sing N N 177 DT "C2'" "C1'" sing N N 178 DT "C2'" "H2'" sing N N 179 DT "C2'" "H2''" sing N N 180 DT "C1'" N1 sing N N 181 DT "C1'" "H1'" sing N N 182 DT N1 C2 sing N N 183 DT N1 C6 sing N N 184 DT C2 O2 doub N N 185 DT C2 N3 sing N N 186 DT N3 C4 sing N N 187 DT N3 H3 sing N N 188 DT C4 O4 doub N N 189 DT C4 C5 sing N N 190 DT C5 C7 sing N N 191 DT C5 C6 doub N N 192 DT C7 H71 sing N N 193 DT C7 H72 sing N N 194 DT C7 H73 sing N N 195 DT C6 H6 sing N N 196 HOH O H1 sing N N 197 HOH O H2 sing N N 198 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3NP6 'double helix' 3NP6 'b-form double helix' 3NP6 '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 -0.241 -0.176 0.041 -12.422 -2.953 1.525 1 B_DG8:DC5_A B 8 ? A 5 ? 19 1 1 B DT 3 1_555 A DA 4 1_555 -0.280 0.105 -0.071 2.974 -5.637 -2.967 2 B_DT9:DA4_A B 9 ? A 4 ? 20 1 1 B DA 4 1_555 A DT 3 1_555 0.194 -0.119 0.147 2.760 -6.299 -2.803 3 B_DA10:DT3_A B 10 ? A 3 ? 20 1 1 B DC 5 1_555 A DG 2 1_555 0.478 -0.087 0.142 5.535 -0.591 3.858 4 B_DC11:DG2_A B 11 ? A 2 ? 19 1 1 C DG 2 1_555 D DC 5 1_555 -0.243 -0.301 0.040 -5.985 0.988 2.581 5 C_DG2:DC11_D C 2 ? D 11 ? 19 1 1 C DT 3 1_555 D DA 4 1_555 -0.474 -0.329 0.306 -0.963 -5.912 -0.672 6 C_DT3:DA10_D C 3 ? D 10 ? 20 1 1 C DA 4 1_555 D DT 3 1_555 -0.109 0.012 0.092 0.480 -1.774 -0.391 7 C_DA4:DT9_D C 4 ? D 9 ? 20 1 1 C DC 5 1_555 D DG 2 1_555 0.457 0.175 -0.123 16.259 3.015 2.526 8 C_DC5:DG8_D C 5 ? D 8 ? 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 -1.025 -0.562 3.061 2.669 1.546 30.479 -1.343 2.424 2.931 2.932 -5.060 30.631 1 BB_DG8DT9:DA4DC5_AA B 8 ? A 5 ? B 9 ? A 4 ? 1 B DT 3 1_555 A DA 4 1_555 B DA 4 1_555 A DT 3 1_555 -0.133 -0.171 3.242 -2.256 2.449 39.916 -0.527 -0.062 3.229 3.581 3.297 40.049 2 BB_DT9DA10:DT3DA4_AA B 9 ? A 4 ? B 10 ? A 3 ? 1 B DA 4 1_555 A DT 3 1_555 B DC 5 1_555 A DG 2 1_555 0.462 -0.197 3.397 -0.239 2.622 28.359 -1.021 -0.996 3.362 5.336 0.487 28.479 3 BB_DA10DC11:DG2DT3_AA B 10 ? A 3 ? B 11 ? A 2 ? 1 B DC 5 1_555 A DG 2 1_555 C DG 2 1_555 D DC 5 1_555 -0.016 0.948 3.516 0.774 4.400 -70.766 -0.980 0.015 3.459 -3.796 0.668 -70.888 4 BC_DC11DG2:DC11DG2_DA B 11 ? A 2 ? C 2 ? D 11 ? 1 C DG 2 1_555 D DC 5 1_555 C DT 3 1_555 D DA 4 1_555 -0.485 -0.440 3.319 -2.016 1.313 24.370 -1.451 0.507 3.320 3.101 4.761 24.487 5 CC_DG2DT3:DA10DC11_DD C 2 ? D 11 ? C 3 ? D 10 ? 1 C DT 3 1_555 D DA 4 1_555 C DA 4 1_555 D DT 3 1_555 0.270 -0.226 3.218 1.970 1.836 40.484 -0.527 -0.173 3.214 2.650 -2.843 40.570 6 CC_DT3DA4:DT9DA10_DD C 3 ? D 10 ? C 4 ? D 9 ? 1 C DA 4 1_555 D DT 3 1_555 C DC 5 1_555 D DG 2 1_555 1.011 -0.509 3.128 -1.075 4.716 30.255 -1.839 -2.114 2.979 8.963 2.044 30.631 7 CC_DA4DC5:DG8DT9_DD C 4 ? D 9 ? C 5 ? D 8 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 BERBERINE BER 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 1XCS _pdbx_initial_refinement_model.details 'PDB ENTRY 1XCS' # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.fraction _pdbx_reflns_twin.operator _pdbx_reflns_twin.type _pdbx_reflns_twin.mean_F_square_over_mean_F2 _pdbx_reflns_twin.mean_I2_over_mean_I_square 1 1 1 0.914 'H, K, L' ? ? ? 2 1 1 0.086 -h,-k,l ? ? ? #