data_432D # _entry.id 432D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 432D pdb_0000432d 10.2210/pdb432d/pdb NDB DD0002 ? ? RCSB RCSB001334 ? ? WWPDB D_1000001334 ? ? # 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 1999-12-18 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-04 5 'Structure model' 1 4 2023-12-27 6 'Structure model' 1 5 2024-04-03 # _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' 'Version format compliance' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' struct_site 6 6 'Structure model' pdbx_initial_refinement_model # 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' '_software.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 432D _pdbx_database_status.recvd_initial_deposition_date 1998-10-14 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Vlieghe, D.' 1 'Van Meervelt, L.' 2 # _citation.id primary _citation.title 'Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode.' _citation.journal_abbrev Biochemistry _citation.journal_volume 38 _citation.page_first 16443 _citation.page_last 16451 _citation.year 1999 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10600105 _citation.pdbx_database_id_DOI 10.1021/bi9907882 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Vlieghe, D.' 1 ? primary 'Sponer, J.' 2 ? primary 'Van Meervelt, L.' 3 ? # 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(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3') ; 3085.029 2 ? ? ? ? 2 non-polymer syn '6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE' 277.324 1 ? ? ? ? 3 water nat water 18.015 81 ? ? ? ? # _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 '(DG)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can GGCCAATTGG _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 '6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE' DAP 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DG n 1 3 DC n 1 4 DC n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DG n 1 10 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DAP non-polymer . '6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE' ? 'C16 H15 N5' 277.324 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 # 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 DG 1 1 1 DG G A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DG 1 11 11 DG G B . n B 1 2 DG 2 12 12 DG G B . n B 1 3 DC 3 13 13 DC C B . n B 1 4 DC 4 14 14 DC C B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 DA 6 16 16 DA A B . n B 1 7 DT 7 17 17 DT T B . n B 1 8 DT 8 18 18 DT T B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DG 10 20 20 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 DAP 1 21 21 DAP DAP A . D 3 HOH 1 22 22 HOH HOH A . D 3 HOH 2 23 23 HOH HOH A . D 3 HOH 3 24 24 HOH HOH A . D 3 HOH 4 31 31 HOH HOH A . D 3 HOH 5 34 34 HOH HOH A . D 3 HOH 6 35 35 HOH HOH A . D 3 HOH 7 36 36 HOH HOH A . D 3 HOH 8 37 37 HOH HOH A . D 3 HOH 9 41 41 HOH HOH A . D 3 HOH 10 44 44 HOH HOH A . D 3 HOH 11 45 45 HOH HOH A . D 3 HOH 12 50 50 HOH HOH A . D 3 HOH 13 51 51 HOH HOH A . D 3 HOH 14 52 52 HOH HOH A . D 3 HOH 15 53 53 HOH HOH A . D 3 HOH 16 54 54 HOH HOH A . D 3 HOH 17 56 56 HOH HOH A . D 3 HOH 18 60 60 HOH HOH A . D 3 HOH 19 62 62 HOH HOH A . D 3 HOH 20 65 65 HOH HOH A . D 3 HOH 21 66 66 HOH HOH A . D 3 HOH 22 67 67 HOH HOH A . D 3 HOH 23 68 68 HOH HOH A . D 3 HOH 24 71 71 HOH HOH A . D 3 HOH 25 73 73 HOH HOH A . D 3 HOH 26 76 76 HOH HOH A . D 3 HOH 27 82 82 HOH HOH A . D 3 HOH 28 89 89 HOH HOH A . D 3 HOH 29 91 91 HOH HOH A . D 3 HOH 30 93 93 HOH HOH A . D 3 HOH 31 94 94 HOH HOH A . D 3 HOH 32 98 98 HOH HOH A . D 3 HOH 33 100 100 HOH HOH A . E 3 HOH 1 25 25 HOH HOH B . E 3 HOH 2 26 26 HOH HOH B . E 3 HOH 3 27 27 HOH HOH B . E 3 HOH 4 28 28 HOH HOH B . E 3 HOH 5 29 29 HOH HOH B . E 3 HOH 6 30 30 HOH HOH B . E 3 HOH 7 32 32 HOH HOH B . E 3 HOH 8 33 33 HOH HOH B . E 3 HOH 9 38 38 HOH HOH B . E 3 HOH 10 39 39 HOH HOH B . E 3 HOH 11 40 40 HOH HOH B . E 3 HOH 12 42 42 HOH HOH B . E 3 HOH 13 43 43 HOH HOH B . E 3 HOH 14 46 46 HOH HOH B . E 3 HOH 15 47 47 HOH HOH B . E 3 HOH 16 48 48 HOH HOH B . E 3 HOH 17 49 49 HOH HOH B . E 3 HOH 18 55 55 HOH HOH B . E 3 HOH 19 57 57 HOH HOH B . E 3 HOH 20 58 58 HOH HOH B . E 3 HOH 21 59 59 HOH HOH B . E 3 HOH 22 61 61 HOH HOH B . E 3 HOH 23 63 63 HOH HOH B . E 3 HOH 24 64 64 HOH HOH B . E 3 HOH 25 69 69 HOH HOH B . E 3 HOH 26 70 70 HOH HOH B . E 3 HOH 27 72 72 HOH HOH B . E 3 HOH 28 74 74 HOH HOH B . E 3 HOH 29 75 75 HOH HOH B . E 3 HOH 30 77 77 HOH HOH B . E 3 HOH 31 78 78 HOH HOH B . E 3 HOH 32 79 79 HOH HOH B . E 3 HOH 33 80 80 HOH HOH B . E 3 HOH 34 81 81 HOH HOH B . E 3 HOH 35 83 83 HOH HOH B . E 3 HOH 36 84 84 HOH HOH B . E 3 HOH 37 85 85 HOH HOH B . E 3 HOH 38 86 86 HOH HOH B . E 3 HOH 39 87 87 HOH HOH B . E 3 HOH 40 88 88 HOH HOH B . E 3 HOH 41 90 90 HOH HOH B . E 3 HOH 42 92 92 HOH HOH B . E 3 HOH 43 95 95 HOH HOH B . E 3 HOH 44 96 96 HOH HOH B . E 3 HOH 45 97 97 HOH HOH B . E 3 HOH 46 99 99 HOH HOH B . E 3 HOH 47 101 101 HOH HOH B . E 3 HOH 48 102 102 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL refinement . ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 # _cell.entry_id 432D _cell.length_a 25.616 _cell.length_b 36.563 _cell.length_c 52.961 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 432D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 # _exptl.entry_id 432D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 36.26 _exptl_crystal.density_Matthews 1.93 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 289.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.9 _exptl_crystal_grow.pdbx_details 'pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'SODIUM CACODYLATE' ? ? ? 1 2 1 MGCL2 ? ? ? 1 3 1 SPERMINE ? ? ? 1 4 1 MPD ? ? ? 1 5 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 120 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1997-06-15 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _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 ? # _reflns.entry_id 432D _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 10.00 _reflns.d_resolution_high 1.89 _reflns.number_obs 4106 _reflns.number_all 4106 _reflns.percent_possible_obs 97.1 _reflns.pdbx_Rmerge_I_obs 0.0730000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 13.78 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.9 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.89 _reflns_shell.d_res_low 1.93 _reflns_shell.percent_possible_all 95.1 _reflns_shell.Rmerge_I_obs 0.2910000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.55 _reflns_shell.pdbx_redundancy 4.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 432D _refine.ls_number_reflns_obs 3562 _refine.ls_number_reflns_all 4106 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 1.89 _refine.ls_percent_reflns_obs 97.1 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all 0.1920000 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _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 ? _refine.ls_number_parameters 2051 _refine.ls_number_restraints 2080 _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _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_ls_cross_valid_method NONE _refine.details ? _refine.pdbx_starting_model 'BD0006 USED AS STARTING MODEL FOR REFINEMENT' _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'TAYLOR AND KENNARD' _refine.pdbx_stereochem_target_val_spec_case 'DAPI DICTIONARY BASED ON CSD' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 432D _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen 0. _refine_analyze.occupancy_sum_non_hydrogen 512. _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 410 _refine_hist.pdbx_number_atoms_ligand 21 _refine_hist.number_atoms_solvent 81 _refine_hist.number_atoms_total 512 _refine_hist.d_res_high 1.89 _refine_hist.d_res_low 10.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.013 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.029 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.023 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.091 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.00 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.082 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.002 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.00 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.038 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.00 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 432D _pdbx_refine.R_factor_all_no_cutoff 0.1920000 _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_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 0.1800000 _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 3562 _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 432D _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 432D _struct.title 'D(GGCCAATTGG) COMPLEXED WITH DAPI' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 432D _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;DEOXYRIBONUCLEIC ACID, DNA-DRUG COMPLEX, TRIPLET FORMATION, 4', 6-DIAMIDINO-2-PHENYL INDOLE, DAPI, MINOR GROOVE BINDER, 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 432D _struct_ref.pdbx_db_accession 432D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 432D A 1 ? 10 ? 432D 1 ? 10 ? 1 10 2 1 432D B 1 ? 10 ? 432D 11 ? 20 ? 11 20 # _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 # _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.pdbx_parent_biol_id ? _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 hydrog1 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 4 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 4 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 4 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 9 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 9 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 9 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 DAP 21 ? 11 'BINDING SITE FOR RESIDUE DAP A 21' 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 11 DT A 7 ? DT A 7 . ? 1_555 ? 2 AC1 11 DT A 8 ? DT A 8 . ? 1_555 ? 3 AC1 11 DG A 9 ? DG A 9 . ? 1_555 ? 4 AC1 11 DG A 10 ? DG A 10 . ? 1_555 ? 5 AC1 11 HOH D . ? HOH A 56 . ? 1_555 ? 6 AC1 11 HOH D . ? HOH A 94 . ? 1_555 ? 7 AC1 11 DA B 6 ? DA B 16 . ? 1_555 ? 8 AC1 11 DT B 7 ? DT B 17 . ? 1_555 ? 9 AC1 11 DT B 8 ? DT B 18 . ? 1_555 ? 10 AC1 11 HOH E . ? HOH B 42 . ? 1_555 ? 11 AC1 11 HOH E . ? HOH B 72 . ? 4_456 ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 DT _pdbx_validate_rmsd_bond.auth_seq_id_1 8 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 DT _pdbx_validate_rmsd_bond.auth_seq_id_2 8 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.488 _pdbx_validate_rmsd_bond.bond_target_value 1.420 _pdbx_validate_rmsd_bond.bond_deviation 0.068 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.011 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A DG 2 ? ? "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 102.63 109.40 -6.77 0.80 N 2 1 "C3'" A DC 4 ? ? "C2'" A DC 4 ? ? "C1'" A DC 4 ? ? 96.39 102.40 -6.01 0.80 N 3 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 111.08 108.30 2.78 0.30 N 4 1 N9 A DA 5 ? ? "C1'" A DA 5 ? ? "C2'" A DA 5 ? ? 123.19 114.30 8.89 1.40 N 5 1 "C3'" A DA 5 ? ? "O3'" A DA 5 ? ? P A DA 6 ? ? 127.26 119.70 7.56 1.20 Y 6 1 "O5'" A DA 6 ? ? "C5'" A DA 6 ? ? "C4'" A DA 6 ? ? 101.36 109.40 -8.04 0.80 N 7 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? "C2'" A DA 6 ? ? 100.97 105.90 -4.93 0.80 N 8 1 N9 A DA 6 ? ? "C1'" A DA 6 ? ? "C2'" A DA 6 ? ? 124.27 114.30 9.97 1.40 N 9 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 103.48 108.00 -4.52 0.70 N 10 1 N1 A DA 6 ? ? C6 A DA 6 ? ? N6 A DA 6 ? ? 124.38 118.60 5.78 0.60 N 11 1 "O5'" A DT 7 ? ? "C5'" A DT 7 ? ? "C4'" A DT 7 ? ? 103.55 109.40 -5.85 0.80 N 12 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? "C2'" A DT 7 ? ? 100.71 105.90 -5.19 0.80 N 13 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 101.77 108.00 -6.23 0.70 N 14 1 "O5'" A DT 8 ? ? "C5'" A DT 8 ? ? "C4'" A DT 8 ? ? 103.99 109.40 -5.41 0.80 N 15 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? "C2'" A DT 8 ? ? 101.03 105.90 -4.87 0.80 N 16 1 N1 A DT 8 ? ? "C1'" A DT 8 ? ? "C2'" A DT 8 ? ? 124.27 114.30 9.97 1.40 N 17 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 96.98 108.00 -11.02 0.70 N 18 1 "C3'" A DT 8 ? ? "O3'" A DT 8 ? ? P A DG 9 ? ? 129.24 119.70 9.54 1.20 Y 19 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 101.45 108.00 -6.55 0.70 N 20 1 N1 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 125.06 119.90 5.16 0.60 N 21 1 C5 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 122.88 128.60 -5.72 0.60 N 22 1 "O5'" A DG 10 ? ? "C5'" A DG 10 ? ? "C4'" A DG 10 ? ? 101.56 109.40 -7.84 0.80 N 23 1 N1 B DC 13 ? ? C2 B DC 13 ? ? O2 B DC 13 ? ? 123.38 118.90 4.48 0.60 N 24 1 "C3'" B DC 14 ? ? "O3'" B DC 14 ? ? P B DA 15 ? ? 127.10 119.70 7.40 1.20 Y 25 1 "C3'" B DA 15 ? ? "C2'" B DA 15 ? ? "C1'" B DA 15 ? ? 97.17 102.40 -5.23 0.80 N 26 1 N1 B DA 15 ? ? C6 B DA 15 ? ? N6 B DA 15 ? ? 122.20 118.60 3.60 0.60 N 27 1 N1 B DT 17 ? ? "C1'" B DT 17 ? ? "C2'" B DT 17 ? ? 124.93 114.30 10.63 1.40 N 28 1 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 99.70 108.00 -8.30 0.70 N 29 1 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? "C2'" B DT 18 ? ? 100.23 105.90 -5.67 0.80 N 30 1 N1 B DT 18 ? ? "C1'" B DT 18 ? ? "C2'" B DT 18 ? ? 124.11 114.30 9.81 1.40 N 31 1 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 100.01 108.00 -7.99 0.70 N 32 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 100.49 108.00 -7.51 0.70 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DAP N1 N Y N 37 DAP C2 C Y N 38 DAP C3 C Y N 39 DAP C4 C Y N 40 DAP C5 C Y N 41 DAP C6 C Y N 42 DAP C7 C Y N 43 DAP C8 C Y N 44 DAP C9 C Y N 45 DAP C10 C N N 46 DAP N2 N N N 47 DAP N3 N N N 48 DAP "C1'" C Y N 49 DAP "C2'" C Y N 50 DAP "C3'" C Y N 51 DAP "C4'" C Y N 52 DAP "C5'" C Y N 53 DAP "C6'" C Y N 54 DAP C11 C N N 55 DAP N4 N N N 56 DAP N5 N N N 57 DAP HN1 H N N 58 DAP H3 H N N 59 DAP H4 H N N 60 DAP H5 H N N 61 DAP H7 H N N 62 DAP HN2 H N N 63 DAP HN31 H N N 64 DAP HN32 H N N 65 DAP "H2'" H N N 66 DAP "H3'" H N N 67 DAP "H5'" H N N 68 DAP "H6'" H N N 69 DAP HN4 H N N 70 DAP HN51 H N N 71 DAP HN52 H N N 72 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 DG OP3 O N N 107 DG P P N N 108 DG OP1 O N N 109 DG OP2 O N N 110 DG "O5'" O N N 111 DG "C5'" C N N 112 DG "C4'" C N R 113 DG "O4'" O N N 114 DG "C3'" C N S 115 DG "O3'" O N N 116 DG "C2'" C N N 117 DG "C1'" C N R 118 DG N9 N Y N 119 DG C8 C Y N 120 DG N7 N Y N 121 DG C5 C Y N 122 DG C6 C N N 123 DG O6 O N N 124 DG N1 N N N 125 DG C2 C N N 126 DG N2 N N N 127 DG N3 N N N 128 DG C4 C Y N 129 DG HOP3 H N N 130 DG HOP2 H N N 131 DG "H5'" H N N 132 DG "H5''" H N N 133 DG "H4'" H N N 134 DG "H3'" H N N 135 DG "HO3'" H N N 136 DG "H2'" H N N 137 DG "H2''" H N N 138 DG "H1'" H N N 139 DG H8 H N N 140 DG H1 H N N 141 DG H21 H N N 142 DG H22 H N N 143 DT OP3 O N N 144 DT P P N N 145 DT OP1 O N N 146 DT OP2 O N N 147 DT "O5'" O N N 148 DT "C5'" C N N 149 DT "C4'" C N R 150 DT "O4'" O N N 151 DT "C3'" C N S 152 DT "O3'" O N N 153 DT "C2'" C N N 154 DT "C1'" C N R 155 DT N1 N N N 156 DT C2 C N N 157 DT O2 O N N 158 DT N3 N N N 159 DT C4 C N N 160 DT O4 O N N 161 DT C5 C N N 162 DT C7 C N N 163 DT C6 C N N 164 DT HOP3 H N N 165 DT HOP2 H N N 166 DT "H5'" H N N 167 DT "H5''" H N N 168 DT "H4'" H N N 169 DT "H3'" H N N 170 DT "HO3'" H N N 171 DT "H2'" H N N 172 DT "H2''" H N N 173 DT "H1'" H N N 174 DT H3 H N N 175 DT H71 H N N 176 DT H72 H N N 177 DT H73 H N N 178 DT H6 H N N 179 HOH O O N N 180 HOH H1 H N N 181 HOH H2 H N N 182 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DAP N1 C2 sing Y N 39 DAP N1 C8 sing Y N 40 DAP N1 HN1 sing N N 41 DAP C2 C3 doub Y N 42 DAP C2 "C1'" sing Y N 43 DAP C3 C9 sing Y N 44 DAP C3 H3 sing N N 45 DAP C4 C5 doub Y N 46 DAP C4 C9 sing Y N 47 DAP C4 H4 sing N N 48 DAP C5 C6 sing Y N 49 DAP C5 H5 sing N N 50 DAP C6 C7 doub Y N 51 DAP C6 C10 sing N N 52 DAP C7 C8 sing Y N 53 DAP C7 H7 sing N N 54 DAP C8 C9 doub Y N 55 DAP C10 N2 doub N N 56 DAP C10 N3 sing N N 57 DAP N2 HN2 sing N N 58 DAP N3 HN31 sing N N 59 DAP N3 HN32 sing N N 60 DAP "C1'" "C2'" doub Y N 61 DAP "C1'" "C6'" sing Y N 62 DAP "C2'" "C3'" sing Y N 63 DAP "C2'" "H2'" sing N N 64 DAP "C3'" "C4'" doub Y N 65 DAP "C3'" "H3'" sing N N 66 DAP "C4'" "C5'" sing Y N 67 DAP "C4'" C11 sing N N 68 DAP "C5'" "C6'" doub Y N 69 DAP "C5'" "H5'" sing N N 70 DAP "C6'" "H6'" sing N N 71 DAP C11 N4 doub N N 72 DAP C11 N5 sing N N 73 DAP N4 HN4 sing N N 74 DAP N5 HN51 sing N N 75 DAP N5 HN52 sing N N 76 DC OP3 P sing N N 77 DC OP3 HOP3 sing N N 78 DC P OP1 doub N N 79 DC P OP2 sing N N 80 DC P "O5'" sing N N 81 DC OP2 HOP2 sing N N 82 DC "O5'" "C5'" sing N N 83 DC "C5'" "C4'" sing N N 84 DC "C5'" "H5'" sing N N 85 DC "C5'" "H5''" sing N N 86 DC "C4'" "O4'" sing N N 87 DC "C4'" "C3'" sing N N 88 DC "C4'" "H4'" sing N N 89 DC "O4'" "C1'" sing N N 90 DC "C3'" "O3'" sing N N 91 DC "C3'" "C2'" sing N N 92 DC "C3'" "H3'" sing N N 93 DC "O3'" "HO3'" sing N N 94 DC "C2'" "C1'" sing N N 95 DC "C2'" "H2'" sing N N 96 DC "C2'" "H2''" sing N N 97 DC "C1'" N1 sing N N 98 DC "C1'" "H1'" sing N N 99 DC N1 C2 sing N N 100 DC N1 C6 sing N N 101 DC C2 O2 doub N N 102 DC C2 N3 sing N N 103 DC N3 C4 doub N N 104 DC C4 N4 sing N N 105 DC C4 C5 sing N N 106 DC N4 H41 sing N N 107 DC N4 H42 sing N N 108 DC C5 C6 doub N N 109 DC C5 H5 sing N N 110 DC C6 H6 sing N N 111 DG OP3 P sing N N 112 DG OP3 HOP3 sing N N 113 DG P OP1 doub N N 114 DG P OP2 sing N N 115 DG P "O5'" sing N N 116 DG OP2 HOP2 sing N N 117 DG "O5'" "C5'" sing N N 118 DG "C5'" "C4'" sing N N 119 DG "C5'" "H5'" sing N N 120 DG "C5'" "H5''" sing N N 121 DG "C4'" "O4'" sing N N 122 DG "C4'" "C3'" sing N N 123 DG "C4'" "H4'" sing N N 124 DG "O4'" "C1'" sing N N 125 DG "C3'" "O3'" sing N N 126 DG "C3'" "C2'" sing N N 127 DG "C3'" "H3'" sing N N 128 DG "O3'" "HO3'" sing N N 129 DG "C2'" "C1'" sing N N 130 DG "C2'" "H2'" sing N N 131 DG "C2'" "H2''" sing N N 132 DG "C1'" N9 sing N N 133 DG "C1'" "H1'" sing N N 134 DG N9 C8 sing Y N 135 DG N9 C4 sing Y N 136 DG C8 N7 doub Y N 137 DG C8 H8 sing N N 138 DG N7 C5 sing Y N 139 DG C5 C6 sing N N 140 DG C5 C4 doub Y N 141 DG C6 O6 doub N N 142 DG C6 N1 sing N N 143 DG N1 C2 sing N N 144 DG N1 H1 sing N N 145 DG C2 N2 sing N N 146 DG C2 N3 doub N N 147 DG N2 H21 sing N N 148 DG N2 H22 sing N N 149 DG N3 C4 sing N N 150 DT OP3 P sing N N 151 DT OP3 HOP3 sing N N 152 DT P OP1 doub N N 153 DT P OP2 sing N N 154 DT P "O5'" sing N N 155 DT OP2 HOP2 sing N N 156 DT "O5'" "C5'" sing N N 157 DT "C5'" "C4'" sing N N 158 DT "C5'" "H5'" sing N N 159 DT "C5'" "H5''" sing N N 160 DT "C4'" "O4'" sing N N 161 DT "C4'" "C3'" sing N N 162 DT "C4'" "H4'" sing N N 163 DT "O4'" "C1'" sing N N 164 DT "C3'" "O3'" sing N N 165 DT "C3'" "C2'" sing N N 166 DT "C3'" "H3'" sing N N 167 DT "O3'" "HO3'" sing N N 168 DT "C2'" "C1'" sing N N 169 DT "C2'" "H2'" sing N N 170 DT "C2'" "H2''" sing N N 171 DT "C1'" N1 sing N N 172 DT "C1'" "H1'" sing N N 173 DT N1 C2 sing N N 174 DT N1 C6 sing N N 175 DT C2 O2 doub N N 176 DT C2 N3 sing N N 177 DT N3 C4 sing N N 178 DT N3 H3 sing N N 179 DT C4 O4 doub N N 180 DT C4 C5 sing N N 181 DT C5 C7 sing N N 182 DT C5 C6 doub N N 183 DT C7 H71 sing N N 184 DT C7 H72 sing N N 185 DT C7 H73 sing N N 186 DT C6 H6 sing N N 187 HOH O H1 sing N N 188 HOH O H2 sing N N 189 # _ndb_struct_conf_na.entry_id 432D _ndb_struct_conf_na.feature 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 3 1_555 B DG 10 1_555 0.114 -0.161 -0.062 7.125 -16.984 -1.120 1 A_DC3:DG20_B A 3 ? B 20 ? 19 1 1 A DC 4 1_555 B DG 9 1_555 0.230 -0.022 -0.346 22.181 -1.469 1.493 2 A_DC4:DG19_B A 4 ? B 19 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.093 -0.089 -0.130 2.031 -16.444 -1.681 3 A_DA5:DT18_B A 5 ? B 18 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 -0.207 -0.224 -0.094 0.867 -18.262 4.007 4 A_DA6:DT17_B A 6 ? B 17 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.167 -0.042 -0.250 5.646 -15.877 7.924 5 A_DT7:DA16_B A 7 ? B 16 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.113 -0.108 -0.155 -11.144 -16.338 7.076 6 A_DT8:DA15_B A 8 ? B 15 ? 20 1 1 A DG 9 1_555 B DC 4 1_555 -0.078 -0.140 0.070 -6.450 -6.899 -3.660 7 A_DG9:DC14_B A 9 ? B 14 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.300 -0.149 0.081 -2.832 -18.618 -2.731 8 A_DG10:DC13_B A 10 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 3 1_555 B DG 10 1_555 A DC 4 1_555 B DG 9 1_555 0.676 0.395 3.075 6.218 10.666 24.834 -1.736 0.081 3.062 23.069 -13.448 27.690 1 AA_DC3DC4:DG19DG20_BB A 3 ? B 20 ? A 4 ? B 19 ? 1 A DC 4 1_555 B DG 9 1_555 A DA 5 1_555 B DT 8 1_555 -0.238 0.741 3.778 0.101 5.903 46.381 0.359 0.309 3.839 7.459 -0.128 46.735 2 AA_DC4DA5:DT18DG19_BB A 4 ? B 19 ? A 5 ? B 18 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.622 -0.063 3.237 0.848 -0.545 35.084 -0.024 -0.905 3.251 -0.904 -1.406 35.098 3 AA_DA5DA6:DT17DT18_BB A 5 ? B 18 ? A 6 ? B 17 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.092 -0.428 3.061 0.358 0.208 31.858 -0.815 -0.106 3.059 0.379 -0.652 31.861 4 AA_DA6DT7:DA16DT17_BB A 6 ? B 17 ? A 7 ? B 16 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 0.495 0.022 3.667 5.710 4.573 41.051 -0.515 -0.014 3.682 6.459 -8.065 41.669 5 AA_DT7DT8:DA15DA16_BB A 7 ? B 16 ? A 8 ? B 15 ? 1 A DT 8 1_555 B DA 5 1_555 A DG 9 1_555 B DC 4 1_555 -0.760 -0.047 3.268 -3.746 6.609 32.477 -1.194 0.695 3.261 11.619 6.585 33.331 6 AA_DT8DG9:DC14DA15_BB A 8 ? B 15 ? A 9 ? B 14 ? 1 A DG 9 1_555 B DC 4 1_555 A DG 10 1_555 B DC 3 1_555 0.222 -0.281 3.264 -0.860 7.599 28.909 -2.102 -0.607 3.084 14.894 1.686 29.882 7 AA_DG9DG10:DC13DC14_BB A 9 ? B 14 ? A 10 ? B 13 ? # _pdbx_initial_refinement_model.accession_code 431D _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.details 'BD0006 USED AS STARTING MODEL FOR REFINEMENT' # _atom_sites.entry_id 432D _atom_sites.fract_transf_matrix[1][1] 0.039038 _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] 0.027350 _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] 0.018882 _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 N O P # loop_