data_3GDD # _entry.id 3GDD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3GDD pdb_00003gdd 10.2210/pdb3gdd/pdb NDB DD0106 ? ? RCSB RCSB051719 ? ? WWPDB D_1000051719 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2010-03-09 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' # 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_struct_conn_angle 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' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.value' 14 3 'Structure model' '_struct_conn.pdbx_dist_value' 15 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 16 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 17 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 19 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 20 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 21 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 22 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 23 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3GDD _pdbx_database_status.recvd_initial_deposition_date 2009-02-24 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Subirana, J.A.' 1 'De Luchi, D.' 2 'Wright, G.' 3 'Gouyette, C.' 4 # _citation.id primary _citation.title 'Structure of a stacked anthraquinone-DNA complex' _citation.journal_abbrev 'Acta Crystallogr.,Sect.F' _citation.journal_volume 66 _citation.page_first 1019 _citation.page_last 1022 _citation.year 2010 _citation.journal_id_ASTM ? _citation.country DK _citation.journal_id_ISSN 1744-3091 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20823516 _citation.pdbx_database_id_DOI 10.1107/S1744309110030034 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'De Luchi, D.' 1 ? primary 'Uson, I.' 2 ? primary 'Wright, G.' 3 ? primary 'Gouyette, C.' 4 ? primary 'Subirana, J.A.' 5 ? # 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(*(BRU)P*AP*GP*G)-3'" 1295.724 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn "N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,7-diyl)bis[2-(dimethylamino)acetamide]" 408.450 4 ? ? ? ? 4 water nat water 18.015 6 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(BRU)(DA)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can UAGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 "N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,7-diyl)bis[2-(dimethylamino)acetamide]" 5BD 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 BRU n 1 2 DA n 1 3 DG n 1 4 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 ;oligonucleotides were synthesized on an automatic synthesizer by the phosphoramidite method. The drug molecule was synthesized starting from the commercial anthraquinone' ; # 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 5BD non-polymer . "N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,7-diyl)bis[2-(dimethylamino)acetamide]" ? 'C22 H24 N4 O4' 408.450 BRU 'DNA linking' n "5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O8 P' 387.078 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 BRU 1 1 1 BRU BRU A . n A 1 2 DA 2 2 2 DA A A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DG 4 4 4 DG G A . n B 1 1 BRU 1 1 1 BRU BRU B . n B 1 2 DA 2 2 2 DA A B . n B 1 3 DG 3 3 3 DG G B . n B 1 4 DG 4 4 4 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MG 1 5 1 MG MG A . D 3 5BD 1 6 1 5BD 5BD A . E 3 5BD 1 7 1 5BD 5BD A . F 3 5BD 1 8 1 5BD 5BD A . G 3 5BD 1 5 1 5BD 5BD B . H 4 HOH 1 9 1 HOH HOH A . H 4 HOH 2 10 2 HOH HOH A . H 4 HOH 3 11 3 HOH HOH A . H 4 HOH 4 12 4 HOH HOH A . H 4 HOH 5 13 5 HOH HOH A . H 4 HOH 6 14 6 HOH HOH A . # 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 N 1 A 5BD 6 ? C17 ? D 5BD 1 C17 2 1 N 1 A 5BD 6 ? C18 ? D 5BD 1 C18 3 1 N 1 A 5BD 6 ? N3 ? D 5BD 1 N3 4 1 N 1 A 5BD 6 ? N4 ? D 5BD 1 N4 5 1 N 1 A 5BD 6 ? C19 ? D 5BD 1 C19 6 1 N 1 A 5BD 6 ? C20 ? D 5BD 1 C20 7 1 N 1 A 5BD 6 ? C21 ? D 5BD 1 C21 8 1 N 1 A 5BD 6 ? C22 ? D 5BD 1 C22 9 1 N 1 A 5BD 7 ? C17 ? E 5BD 1 C17 10 1 N 1 A 5BD 7 ? C18 ? E 5BD 1 C18 11 1 N 1 A 5BD 7 ? N3 ? E 5BD 1 N3 12 1 N 1 A 5BD 7 ? N4 ? E 5BD 1 N4 13 1 N 1 A 5BD 7 ? C19 ? E 5BD 1 C19 14 1 N 1 A 5BD 7 ? C20 ? E 5BD 1 C20 15 1 N 1 A 5BD 7 ? C21 ? E 5BD 1 C21 16 1 N 1 A 5BD 7 ? C22 ? E 5BD 1 C22 17 1 N 1 A 5BD 8 ? C17 ? F 5BD 1 C17 18 1 N 1 A 5BD 8 ? C18 ? F 5BD 1 C18 19 1 N 1 A 5BD 8 ? N3 ? F 5BD 1 N3 20 1 N 1 A 5BD 8 ? N4 ? F 5BD 1 N4 21 1 N 1 A 5BD 8 ? C19 ? F 5BD 1 C19 22 1 N 1 A 5BD 8 ? C20 ? F 5BD 1 C20 23 1 N 1 A 5BD 8 ? C21 ? F 5BD 1 C21 24 1 N 1 A 5BD 8 ? C22 ? F 5BD 1 C22 25 1 N 1 B 5BD 5 ? C17 ? G 5BD 1 C17 26 1 N 1 B 5BD 5 ? C18 ? G 5BD 1 C18 27 1 N 1 B 5BD 5 ? N3 ? G 5BD 1 N3 28 1 N 1 B 5BD 5 ? N4 ? G 5BD 1 N4 29 1 N 1 B 5BD 5 ? C19 ? G 5BD 1 C19 30 1 N 1 B 5BD 5 ? C20 ? G 5BD 1 C20 31 1 N 1 B 5BD 5 ? C21 ? G 5BD 1 C21 32 1 N 1 B 5BD 5 ? C22 ? G 5BD 1 C22 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SOLVE phasing . ? 1 REFMAC refinement 5.2.0019 ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 # _cell.entry_id 3GDD _cell.length_a 29.698 _cell.length_b 29.698 _cell.length_c 60.883 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3GDD _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3GDD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.59 _exptl_crystal.density_percent_sol 52.51 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details '22 mM cacodylate, 0.8 mM magnesium chloride, 15 mM sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2002-05-08 _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 monochromator' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.907 1.0 2 0.921 1.0 3 0.920 1.0 4 0.861 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM16' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM16 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.907,0.921,0.920,0.861 # _reflns.entry_id 3GDD _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 21.26 _reflns.d_resolution_high 2.8 _reflns.number_obs 757 _reflns.number_all 760 _reflns.percent_possible_obs 99.01 _reflns.pdbx_Rmerge_I_obs 0.060 _reflns.pdbx_Rsym_value 0.035 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.9 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.8 _reflns_shell.d_res_low 2.89 _reflns_shell.percent_possible_all 90.9 _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 ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3GDD _refine.ls_number_reflns_obs 757 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 21.26 _refine.ls_d_res_high 2.80 _refine.ls_percent_reflns_obs 99.01 _refine.ls_R_factor_obs 0.23335 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23202 _refine.ls_R_factor_R_free 0.25926 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 41 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.925 _refine.correlation_coeff_Fo_to_Fc_free 0.908 _refine.B_iso_mean 40.120 _refine.aniso_B[1][1] 2.41 _refine.aniso_B[2][2] 2.41 _refine.aniso_B[3][3] -4.82 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'The structure was solved in P43 space group and then refined in P 43 21 2' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free 0.434 _refine.overall_SU_ML 0.261 _refine.overall_SU_B 30.138 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_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 164 _refine_hist.pdbx_number_atoms_ligand 89 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 259 _refine_hist.d_res_high 2.80 _refine_hist.d_res_low 21.26 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.006 0.020 ? 286 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.769 3.000 ? 418 'X-RAY DIFFRACTION' ? r_chiral_restr 0.059 0.200 ? 30 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.002 0.020 ? 178 'X-RAY DIFFRACTION' ? r_nbd_refined 0.266 0.200 ? 85 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.338 0.200 ? 165 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.137 0.200 ? 5 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.161 0.200 ? 78 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.090 0.200 ? 3 'X-RAY DIFFRACTION' ? r_mcbond_it 6.969 1.500 ? 4 'X-RAY DIFFRACTION' ? r_scbond_it 0.651 3.000 ? 281 'X-RAY DIFFRACTION' ? r_scangle_it 1.060 4.500 ? 418 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.803 _refine_ls_shell.d_res_low 2.875 _refine_ls_shell.number_reflns_R_work 50 _refine_ls_shell.R_factor_R_work 0.430 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.164 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 1 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3GDD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 3GDD _struct.title 'An inverted anthraquinone-DNA crystal structure' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3GDD _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'anthraquinone, telomere DNA sequence, drug-DNA complex, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3GDD _struct_ref.pdbx_db_accession 3GDD _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code UAGG _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 3GDD A 1 ? 4 ? 3GDD 1 ? 4 ? 1 4 2 1 3GDD B 1 ? 4 ? 3GDD 1 ? 4 ? 1 4 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _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 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A BRU 1 "O3'" ? ? ? 1_555 A DA 2 P ? ? A BRU 1 A DA 2 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? B BRU 1 "O3'" ? ? ? 1_555 B DA 2 P ? ? B BRU 1 B DA 2 1_555 ? ? ? ? ? ? ? 1.601 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 D 5BD . O4 ? ? A MG 5 A 5BD 6 1_555 ? ? ? ? ? ? ? 2.186 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 5 A HOH 9 1_555 ? ? ? ? ? ? ? 1.995 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 5 A HOH 10 1_555 ? ? ? ? ? ? ? 2.000 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 5 A HOH 11 1_555 ? ? ? ? ? ? ? 2.003 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 5 A HOH 12 1_555 ? ? ? ? ? ? ? 2.000 ? ? hydrog1 hydrog ? ? A BRU 1 N3 ? ? ? 1_555 B DA 2 N1 ? ? A BRU 1 B DA 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A BRU 1 O4 ? ? ? 1_555 B DA 2 N6 ? ? A BRU 1 B DA 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O4 ? D 5BD . ? A 5BD 6 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 9 ? 1_555 125.8 ? 2 O4 ? D 5BD . ? A 5BD 6 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 10 ? 1_555 74.4 ? 3 O ? H HOH . ? A HOH 9 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 10 ? 1_555 144.4 ? 4 O4 ? D 5BD . ? A 5BD 6 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 11 ? 1_555 126.3 ? 5 O ? H HOH . ? A HOH 9 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 11 ? 1_555 66.8 ? 6 O ? H HOH . ? A HOH 10 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 11 ? 1_555 77.6 ? 7 O4 ? D 5BD . ? A 5BD 6 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 12 ? 1_555 80.7 ? 8 O ? H HOH . ? A HOH 9 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 12 ? 1_555 74.1 ? 9 O ? H HOH . ? A HOH 10 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 12 ? 1_555 82.1 ? 10 O ? H HOH . ? A HOH 11 ? 1_555 MG ? C MG . ? A MG 5 ? 1_555 O ? H HOH . ? A HOH 12 ? 1_555 50.5 ? # 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 MG 5 ? 6 'BINDING SITE FOR RESIDUE MG A 5' AC2 Software A 5BD 6 ? 9 'BINDING SITE FOR RESIDUE 5BD A 6' AC3 Software A 5BD 7 ? 3 'BINDING SITE FOR RESIDUE 5BD A 7' AC4 Software A 5BD 8 ? 6 'BINDING SITE FOR RESIDUE 5BD A 8' AC5 Software B 5BD 5 ? 4 'BINDING SITE FOR RESIDUE 5BD B 5' 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 6 5BD D . ? 5BD A 6 . ? 1_555 ? 2 AC1 6 HOH H . ? HOH A 9 . ? 1_555 ? 3 AC1 6 HOH H . ? HOH A 10 . ? 1_555 ? 4 AC1 6 HOH H . ? HOH A 11 . ? 1_555 ? 5 AC1 6 HOH H . ? HOH A 12 . ? 1_555 ? 6 AC1 6 DG B 4 ? DG B 4 . ? 8_665 ? 7 AC2 9 BRU A 1 ? BRU A 1 . ? 5_645 ? 8 AC2 9 MG C . ? MG A 5 . ? 1_555 ? 9 AC2 9 5BD E . ? 5BD A 7 . ? 1_555 ? 10 AC2 9 HOH H . ? HOH A 10 . ? 1_555 ? 11 AC2 9 HOH H . ? HOH A 12 . ? 1_555 ? 12 AC2 9 HOH H . ? HOH A 14 . ? 1_555 ? 13 AC2 9 DA B 2 ? DA B 2 . ? 5_645 ? 14 AC2 9 DG B 3 ? DG B 3 . ? 5_645 ? 15 AC2 9 DG B 4 ? DG B 4 . ? 5_645 ? 16 AC3 3 DG A 3 ? DG A 3 . ? 1_555 ? 17 AC3 3 5BD D . ? 5BD A 6 . ? 1_555 ? 18 AC3 3 DG B 3 ? DG B 3 . ? 8_665 ? 19 AC4 6 DG A 3 ? DG A 3 . ? 1_555 ? 20 AC4 6 HOH H . ? HOH A 13 . ? 1_555 ? 21 AC4 6 DG B 3 ? DG B 3 . ? 8_665 ? 22 AC4 6 DG B 4 ? DG B 4 . ? 8_665 ? 23 AC4 6 5BD G . ? 5BD B 5 . ? 8_665 ? 24 AC4 6 5BD G . ? 5BD B 5 . ? 1_555 ? 25 AC5 4 5BD F . ? 5BD A 8 . ? 1_555 ? 26 AC5 4 5BD F . ? 5BD A 8 . ? 8_665 ? 27 AC5 4 DG B 4 ? DG B 4 . ? 8_665 ? 28 AC5 4 DG B 4 ? DG B 4 . ? 1_555 ? # 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 DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 110.16 108.30 1.86 0.30 N 2 1 "O4'" B DA 2 ? ? "C1'" B DA 2 ? ? N9 B DA 2 ? ? 110.18 108.30 1.88 0.30 N 3 1 "C3'" B DG 3 ? ? "C2'" B DG 3 ? ? "C1'" B DG 3 ? ? 97.00 102.40 -5.40 0.80 N 4 1 "O4'" B DG 3 ? ? "C1'" B DG 3 ? ? N9 B DG 3 ? ? 110.75 108.30 2.45 0.30 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A BRU 1 A BRU 1 ? DU ? 2 B BRU 1 B BRU 1 ? DU ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'OUTSIDE BINDER' # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id 5BD _pdbx_struct_special_symmetry.auth_seq_id 5 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id G _pdbx_struct_special_symmetry.label_comp_id 5BD _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 26.7634 _pdbx_refine_tls.origin_y 1.6050 _pdbx_refine_tls.origin_z 21.8318 _pdbx_refine_tls.T[1][1] 0.0309 _pdbx_refine_tls.T[2][2] 0.0649 _pdbx_refine_tls.T[3][3] 0.1570 _pdbx_refine_tls.T[1][2] 0.0495 _pdbx_refine_tls.T[1][3] 0.0301 _pdbx_refine_tls.T[2][3] -0.0119 _pdbx_refine_tls.L[1][1] 2.2525 _pdbx_refine_tls.L[2][2] 1.3647 _pdbx_refine_tls.L[3][3] 13.2061 _pdbx_refine_tls.L[1][2] 1.2870 _pdbx_refine_tls.L[1][3] 1.9582 _pdbx_refine_tls.L[2][3] -1.5720 _pdbx_refine_tls.S[1][1] -0.1127 _pdbx_refine_tls.S[1][2] -0.0930 _pdbx_refine_tls.S[1][3] -0.2360 _pdbx_refine_tls.S[2][1] 0.1022 _pdbx_refine_tls.S[2][2] 0.4100 _pdbx_refine_tls.S[2][3] -0.0613 _pdbx_refine_tls.S[3][1] 0.3814 _pdbx_refine_tls.S[3][2] -0.5061 _pdbx_refine_tls.S[3][3] -0.2974 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.pdbx_refine_id 1 1 A 1 ? ? A 4 ? ? ? ? 'X-RAY DIFFRACTION' 2 1 B 1 ? ? B 4 ? ? ? ? 'X-RAY DIFFRACTION' 3 1 A 1 ? ? A 6 ? ? ? ? 'X-RAY DIFFRACTION' 4 1 A 1 ? ? A 7 ? ? ? ? 'X-RAY DIFFRACTION' 5 1 A 1 ? ? A 8 ? ? ? ? 'X-RAY DIFFRACTION' 6 1 B 1 ? ? B 5 ? ? ? ? 'X-RAY DIFFRACTION' 7 1 A 1 ? ? A 7 ? ? ? ? 'X-RAY DIFFRACTION' 8 1 I 1 ? ? I 2 ? ? ? ? 'X-RAY DIFFRACTION' # 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 5BD C1 C Y N 1 5BD C2 C Y N 2 5BD C3 C Y N 3 5BD C5 C Y N 4 5BD C6 C Y N 5 5BD C7 C Y N 6 5BD C8 C Y N 7 5BD C9 C N N 8 5BD C11 C Y N 9 5BD C12 C Y N 10 5BD C13 C N N 11 5BD C14 C N N 12 5BD O1 O N N 13 5BD N1 N N N 14 5BD C4 C Y N 15 5BD O2 O N N 16 5BD O3 O N N 17 5BD C15 C Y N 18 5BD C16 C Y N 19 5BD N2 N N N 20 5BD C10 C N N 21 5BD O4 O N N 22 5BD H1 H N N 23 5BD H2 H N N 24 5BD H5 H N N 25 5BD H7 H N N 26 5BD H8 H N N 27 5BD C17 C N N 28 5BD H4 H N N 29 5BD HN2 H N N 30 5BD C18 C N N 31 5BD H81 H N N 32 5BD H9 H N N 33 5BD N3 N N N 34 5BD H10 H N N 35 5BD H11 H N N 36 5BD H12 H N N 37 5BD N4 N N N 38 5BD C19 C N N 39 5BD C20 C N N 40 5BD H13 H N N 41 5BD H14 H N N 42 5BD H15 H N N 43 5BD H16 H N N 44 5BD H17 H N N 45 5BD H18 H N N 46 5BD C21 C N N 47 5BD C22 C N N 48 5BD H19 H N N 49 5BD H20 H N N 50 5BD H21 H N N 51 5BD H22 H N N 52 5BD H23 H N N 53 5BD H24 H N N 54 BRU N1 N N N 55 BRU C2 C N N 56 BRU N3 N N N 57 BRU C4 C N N 58 BRU C5 C N N 59 BRU C6 C N N 60 BRU O2 O N N 61 BRU O4 O N N 62 BRU BR BR N N 63 BRU "C1'" C N R 64 BRU "C2'" C N N 65 BRU "C3'" C N S 66 BRU "C4'" C N R 67 BRU "O3'" O N N 68 BRU "O4'" O N N 69 BRU "C5'" C N N 70 BRU "O5'" O N N 71 BRU P P N N 72 BRU OP1 O N N 73 BRU OP2 O N N 74 BRU OP3 O N N 75 BRU HN3 H N N 76 BRU H6 H N N 77 BRU "H1'" H N N 78 BRU "H2'" H N N 79 BRU "H2''" H N N 80 BRU "H3'" H N N 81 BRU "H4'" H N N 82 BRU "HO3'" H N N 83 BRU "H5'" H N N 84 BRU "H5''" H N N 85 BRU HOP2 H N N 86 BRU HOP3 H N N 87 DA OP3 O N N 88 DA P P N N 89 DA OP1 O N N 90 DA OP2 O N N 91 DA "O5'" O N N 92 DA "C5'" C N N 93 DA "C4'" C N R 94 DA "O4'" O N N 95 DA "C3'" C N S 96 DA "O3'" O N N 97 DA "C2'" C N N 98 DA "C1'" C N R 99 DA N9 N Y N 100 DA C8 C Y N 101 DA N7 N Y N 102 DA C5 C Y N 103 DA C6 C Y N 104 DA N6 N N N 105 DA N1 N Y N 106 DA C2 C Y N 107 DA N3 N Y N 108 DA C4 C Y N 109 DA HOP3 H N N 110 DA HOP2 H N N 111 DA "H5'" H N N 112 DA "H5''" H N N 113 DA "H4'" H N N 114 DA "H3'" H N N 115 DA "HO3'" H N N 116 DA "H2'" H N N 117 DA "H2''" H N N 118 DA "H1'" H N N 119 DA H8 H N N 120 DA H61 H N N 121 DA H62 H N N 122 DA H2 H N N 123 DG OP3 O N N 124 DG P P N N 125 DG OP1 O N N 126 DG OP2 O N N 127 DG "O5'" O N N 128 DG "C5'" C N N 129 DG "C4'" C N R 130 DG "O4'" O N N 131 DG "C3'" C N S 132 DG "O3'" O N N 133 DG "C2'" C N N 134 DG "C1'" C N R 135 DG N9 N Y N 136 DG C8 C Y N 137 DG N7 N Y N 138 DG C5 C Y N 139 DG C6 C N N 140 DG O6 O N N 141 DG N1 N N N 142 DG C2 C N N 143 DG N2 N N N 144 DG N3 N N N 145 DG C4 C Y N 146 DG HOP3 H N N 147 DG HOP2 H N N 148 DG "H5'" H N N 149 DG "H5''" H N N 150 DG "H4'" H N N 151 DG "H3'" H N N 152 DG "HO3'" H N N 153 DG "H2'" H N N 154 DG "H2''" H N N 155 DG "H1'" H N N 156 DG H8 H N N 157 DG H1 H N N 158 DG H21 H N N 159 DG H22 H N N 160 HOH O O N N 161 HOH H1 H N N 162 HOH H2 H N N 163 MG MG MG N N 164 # 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 5BD C1 C2 doub Y N 1 5BD C1 C11 sing Y N 2 5BD C1 H1 sing N N 3 5BD C2 C3 sing Y N 4 5BD C2 H2 sing N N 5 5BD C3 N1 sing N N 6 5BD C3 C4 doub Y N 7 5BD C5 C6 doub Y N 8 5BD C5 C16 sing Y N 9 5BD C5 H5 sing N N 10 5BD C6 C7 sing Y N 11 5BD C6 N2 sing N N 12 5BD C7 C8 doub Y N 13 5BD C7 H7 sing N N 14 5BD C8 C15 sing Y N 15 5BD C8 H8 sing N N 16 5BD C9 O1 doub N N 17 5BD C9 N1 sing N N 18 5BD C9 C17 sing N N 19 5BD C11 C12 doub Y N 20 5BD C11 C14 sing N N 21 5BD C12 C13 sing N N 22 5BD C12 C4 sing Y N 23 5BD C13 O2 doub N N 24 5BD C13 C16 sing N N 25 5BD C14 O3 doub N N 26 5BD C14 C15 sing N N 27 5BD N1 H81 sing N N 28 5BD C4 H4 sing N N 29 5BD C15 C16 doub Y N 30 5BD N2 C10 sing N N 31 5BD N2 HN2 sing N N 32 5BD C10 O4 doub N N 33 5BD C10 C18 sing N N 34 5BD C17 H9 sing N N 35 5BD C17 N3 sing N N 36 5BD C17 H10 sing N N 37 5BD C18 H11 sing N N 38 5BD C18 H12 sing N N 39 5BD C18 N4 sing N N 40 5BD N3 C19 sing N N 41 5BD N3 C20 sing N N 42 5BD N4 C21 sing N N 43 5BD N4 C22 sing N N 44 5BD C19 H16 sing N N 45 5BD C19 H17 sing N N 46 5BD C19 H18 sing N N 47 5BD C20 H13 sing N N 48 5BD C20 H14 sing N N 49 5BD C20 H15 sing N N 50 5BD C21 H19 sing N N 51 5BD C21 H20 sing N N 52 5BD C21 H21 sing N N 53 5BD C22 H22 sing N N 54 5BD C22 H23 sing N N 55 5BD C22 H24 sing N N 56 BRU N1 C2 sing N N 57 BRU N1 C6 sing N N 58 BRU N1 "C1'" sing N N 59 BRU C2 N3 sing N N 60 BRU C2 O2 doub N N 61 BRU N3 C4 sing N N 62 BRU N3 HN3 sing N N 63 BRU C4 C5 sing N N 64 BRU C4 O4 doub N N 65 BRU C5 C6 doub N N 66 BRU C5 BR sing N N 67 BRU C6 H6 sing N N 68 BRU "C1'" "C2'" sing N N 69 BRU "C1'" "O4'" sing N N 70 BRU "C1'" "H1'" sing N N 71 BRU "C2'" "C3'" sing N N 72 BRU "C2'" "H2'" sing N N 73 BRU "C2'" "H2''" sing N N 74 BRU "C3'" "C4'" sing N N 75 BRU "C3'" "O3'" sing N N 76 BRU "C3'" "H3'" sing N N 77 BRU "C4'" "O4'" sing N N 78 BRU "C4'" "C5'" sing N N 79 BRU "C4'" "H4'" sing N N 80 BRU "O3'" "HO3'" sing N N 81 BRU "C5'" "O5'" sing N N 82 BRU "C5'" "H5'" sing N N 83 BRU "C5'" "H5''" sing N N 84 BRU "O5'" P sing N N 85 BRU P OP1 doub N N 86 BRU P OP2 sing N N 87 BRU P OP3 sing N N 88 BRU OP2 HOP2 sing N N 89 BRU OP3 HOP3 sing N N 90 DA OP3 P sing N N 91 DA OP3 HOP3 sing N N 92 DA P OP1 doub N N 93 DA P OP2 sing N N 94 DA P "O5'" sing N N 95 DA OP2 HOP2 sing N N 96 DA "O5'" "C5'" sing N N 97 DA "C5'" "C4'" sing N N 98 DA "C5'" "H5'" sing N N 99 DA "C5'" "H5''" sing N N 100 DA "C4'" "O4'" sing N N 101 DA "C4'" "C3'" sing N N 102 DA "C4'" "H4'" sing N N 103 DA "O4'" "C1'" sing N N 104 DA "C3'" "O3'" sing N N 105 DA "C3'" "C2'" sing N N 106 DA "C3'" "H3'" sing N N 107 DA "O3'" "HO3'" sing N N 108 DA "C2'" "C1'" sing N N 109 DA "C2'" "H2'" sing N N 110 DA "C2'" "H2''" sing N N 111 DA "C1'" N9 sing N N 112 DA "C1'" "H1'" sing N N 113 DA N9 C8 sing Y N 114 DA N9 C4 sing Y N 115 DA C8 N7 doub Y N 116 DA C8 H8 sing N N 117 DA N7 C5 sing Y N 118 DA C5 C6 sing Y N 119 DA C5 C4 doub Y N 120 DA C6 N6 sing N N 121 DA C6 N1 doub Y N 122 DA N6 H61 sing N N 123 DA N6 H62 sing N N 124 DA N1 C2 sing Y N 125 DA C2 N3 doub Y N 126 DA C2 H2 sing N N 127 DA N3 C4 sing Y N 128 DG OP3 P sing N N 129 DG OP3 HOP3 sing N N 130 DG P OP1 doub N N 131 DG P OP2 sing N N 132 DG P "O5'" sing N N 133 DG OP2 HOP2 sing N N 134 DG "O5'" "C5'" sing N N 135 DG "C5'" "C4'" sing N N 136 DG "C5'" "H5'" sing N N 137 DG "C5'" "H5''" sing N N 138 DG "C4'" "O4'" sing N N 139 DG "C4'" "C3'" sing N N 140 DG "C4'" "H4'" sing N N 141 DG "O4'" "C1'" sing N N 142 DG "C3'" "O3'" sing N N 143 DG "C3'" "C2'" sing N N 144 DG "C3'" "H3'" sing N N 145 DG "O3'" "HO3'" sing N N 146 DG "C2'" "C1'" sing N N 147 DG "C2'" "H2'" sing N N 148 DG "C2'" "H2''" sing N N 149 DG "C1'" N9 sing N N 150 DG "C1'" "H1'" sing N N 151 DG N9 C8 sing Y N 152 DG N9 C4 sing Y N 153 DG C8 N7 doub Y N 154 DG C8 H8 sing N N 155 DG N7 C5 sing Y N 156 DG C5 C6 sing N N 157 DG C5 C4 doub Y N 158 DG C6 O6 doub N N 159 DG C6 N1 sing N N 160 DG N1 C2 sing N N 161 DG N1 H1 sing N N 162 DG C2 N2 sing N N 163 DG C2 N3 doub N N 164 DG N2 H21 sing N N 165 DG N2 H22 sing N N 166 DG N3 C4 sing N N 167 HOH O H1 sing N N 168 HOH O H2 sing N N 169 # _ndb_struct_conf_na.entry_id 3GDD _ndb_struct_conf_na.feature 'double helix' # _ndb_struct_na_base_pair.model_number 1 _ndb_struct_na_base_pair.i_label_asym_id A _ndb_struct_na_base_pair.i_label_comp_id BRU _ndb_struct_na_base_pair.i_label_seq_id 1 _ndb_struct_na_base_pair.i_symmetry 1_555 _ndb_struct_na_base_pair.j_label_asym_id B _ndb_struct_na_base_pair.j_label_comp_id DA _ndb_struct_na_base_pair.j_label_seq_id 2 _ndb_struct_na_base_pair.j_symmetry 1_555 _ndb_struct_na_base_pair.shear 0.155 _ndb_struct_na_base_pair.stretch 0.039 _ndb_struct_na_base_pair.stagger -0.642 _ndb_struct_na_base_pair.buckle 22.616 _ndb_struct_na_base_pair.propeller -15.226 _ndb_struct_na_base_pair.opening 3.350 _ndb_struct_na_base_pair.pair_number 1 _ndb_struct_na_base_pair.pair_name A_BRU1:DA2_B _ndb_struct_na_base_pair.i_auth_asym_id A _ndb_struct_na_base_pair.i_auth_seq_id 1 _ndb_struct_na_base_pair.i_PDB_ins_code ? _ndb_struct_na_base_pair.j_auth_asym_id B _ndb_struct_na_base_pair.j_auth_seq_id 2 _ndb_struct_na_base_pair.j_PDB_ins_code ? _ndb_struct_na_base_pair.hbond_type_28 20 _ndb_struct_na_base_pair.hbond_type_12 1 # _atom_sites.entry_id 3GDD _atom_sites.fract_transf_matrix[1][1] 0.033672 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033672 _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] 0.016425 _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 BR C MG N O P # loop_