data_245D # _entry.id 245D # _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 245D pdb_0000245d 10.2210/pdb245d/pdb RCSB DDF063 ? ? WWPDB D_1000177641 ? ? # 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 1996-02-07 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 245D _pdbx_database_status.recvd_initial_deposition_date 1996-01-12 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Schuerman, G.S.' 1 'Smith, C.K.' 2 'Turkenburg, J.P.' 3 'Dettmar, A.N.' 4 'Van Meervelt, L.' 5 'Moore, M.H.' 6 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;DNA-drug refinement: a comparison of the programs NUCLSQ, PROLSQ, SHELXL93 and X-PLOR, using the low-temperature d(TGATCA)-nogalamycin structure. ; 'Acta Crystallogr.,Sect.D' 52 299 314 1996 ABCRE6 DK 0907-4449 0766 ? 15299703 10.1107/S0907444995012261 1 'DNA-Nogalamycin Interactions: The Crystal Structure of d(TGATCA) Complexed with Nogalamycin' Biochemistry 34 415 425 1995 BICHAW US 0006-2960 0033 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Schuerman, G.S.' 1 ? primary 'Smith, C.K.' 2 ? primary 'Turkenburg, J.P.' 3 ? primary 'Dettmar, A.N.' 4 ? primary 'Van Meervelt, L.' 5 ? primary 'Moore, M.H.' 6 ? 1 'Smith, C.K.' 7 ? 1 'Davies, G.J.' 8 ? 1 'Dodson, E.J.' 9 ? 1 'Moore, M.H.' 10 ? # 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(*TP*GP*AP*TP*CP*A)-3') ; 1808.229 2 ? ? ? ? 2 non-polymer syn NOGALAMYCIN 787.803 2 ? ? ? ? 3 water nat water 18.015 66 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DT)(DG)(DA)(DT)(DC)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TGATCA _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 NOGALAMYCIN NGM 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DG n 1 3 DA n 1 4 DT n 1 5 DC n 1 6 DA 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 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 NGM non-polymer . NOGALAMYCIN ? 'C39 H49 N O16' 787.803 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DT 1 1 1 DT T A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DA 6 6 6 DA A A . n B 1 1 DT 1 7 7 DT T B . n B 1 2 DG 2 8 8 DG G B . n B 1 3 DA 3 9 9 DA A B . n B 1 4 DT 4 10 10 DT T B . n B 1 5 DC 5 11 11 DC C B . n B 1 6 DA 6 12 12 DA A 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 NGM 1 14 14 NGM NGM A . D 2 NGM 1 13 13 NGM NGM B . E 3 HOH 1 16 16 HOH HOH A . E 3 HOH 2 18 18 HOH HOH A . E 3 HOH 3 19 19 HOH HOH A . E 3 HOH 4 20 20 HOH HOH A . E 3 HOH 5 21 21 HOH HOH A . E 3 HOH 6 22 22 HOH HOH A . E 3 HOH 7 24 24 HOH HOH A . E 3 HOH 8 25 25 HOH HOH A . E 3 HOH 9 29 29 HOH HOH A . E 3 HOH 10 31 31 HOH HOH A . E 3 HOH 11 32 32 HOH HOH A . E 3 HOH 12 33 33 HOH HOH A . E 3 HOH 13 34 34 HOH HOH A . E 3 HOH 14 35 35 HOH HOH A . E 3 HOH 15 36 36 HOH HOH A . E 3 HOH 16 37 37 HOH HOH A . E 3 HOH 17 42 42 HOH HOH A . E 3 HOH 18 43 43 HOH HOH A . E 3 HOH 19 44 44 HOH HOH A . E 3 HOH 20 47 47 HOH HOH A . E 3 HOH 21 48 48 HOH HOH A . E 3 HOH 22 51 51 HOH HOH A . E 3 HOH 23 52 52 HOH HOH A . E 3 HOH 24 53 53 HOH HOH A . E 3 HOH 25 54 54 HOH HOH A . E 3 HOH 26 55 55 HOH HOH A . E 3 HOH 27 58 58 HOH HOH A . E 3 HOH 28 59 59 HOH HOH A . E 3 HOH 29 60 60 HOH HOH A . E 3 HOH 30 61 61 HOH HOH A . E 3 HOH 31 63 63 HOH HOH A . E 3 HOH 32 66 66 HOH HOH A . E 3 HOH 33 67 67 HOH HOH A . E 3 HOH 34 68 68 HOH HOH A . E 3 HOH 35 69 69 HOH HOH A . E 3 HOH 36 72 72 HOH HOH A . E 3 HOH 37 73 73 HOH HOH A . E 3 HOH 38 74 74 HOH HOH A . E 3 HOH 39 76 76 HOH HOH A . E 3 HOH 40 77 77 HOH HOH A . E 3 HOH 41 78 78 HOH HOH A . E 3 HOH 42 79 79 HOH HOH A . E 3 HOH 43 80 80 HOH HOH A . F 3 HOH 1 15 15 HOH HOH B . F 3 HOH 2 17 17 HOH HOH B . F 3 HOH 3 23 23 HOH HOH B . F 3 HOH 4 26 26 HOH HOH B . F 3 HOH 5 27 27 HOH HOH B . F 3 HOH 6 28 28 HOH HOH B . F 3 HOH 7 30 30 HOH HOH B . F 3 HOH 8 38 38 HOH HOH B . F 3 HOH 9 39 39 HOH HOH B . F 3 HOH 10 40 40 HOH HOH B . F 3 HOH 11 41 41 HOH HOH B . F 3 HOH 12 45 45 HOH HOH B . F 3 HOH 13 46 46 HOH HOH B . F 3 HOH 14 49 49 HOH HOH B . F 3 HOH 15 50 50 HOH HOH B . F 3 HOH 16 56 56 HOH HOH B . F 3 HOH 17 57 57 HOH HOH B . F 3 HOH 18 62 62 HOH HOH B . F 3 HOH 19 64 64 HOH HOH B . F 3 HOH 20 65 65 HOH HOH B . F 3 HOH 21 70 70 HOH HOH B . F 3 HOH 22 71 71 HOH HOH B . F 3 HOH 23 75 75 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-93 refinement . ? 1 DENZO 'data reduction' . ? 2 CCP4 'data reduction' . ? 3 # _cell.entry_id 245D _cell.length_a 37.290 _cell.length_b 37.290 _cell.length_c 71.120 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 245D _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 # _exptl.entry_id 245D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.42 _exptl_crystal.density_percent_sol 64.02 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.50 _exptl_crystal_grow.pdbx_details 'pH 6.50, VAPOR DIFFUSION, HANGING DROP' _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 WATER ? ? ? 1 2 1 HMD ? ? ? 1 3 1 SPERMINE ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 1 'NA CACODYLATE' ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 150.00 _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 ? _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 ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.87 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SRS BEAMLINE PX9.6' _diffrn_source.pdbx_synchrotron_site SRS _diffrn_source.pdbx_synchrotron_beamline PX9.6 _diffrn_source.pdbx_wavelength 0.87 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 245D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 1.400 _reflns.number_obs 10306 _reflns.number_all 62880 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs 0.0360000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 245D _refine.ls_number_reflns_obs 9813 _refine.ls_number_reflns_all 9813 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 1.400 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1600000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.2520000 _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 ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 18.80 _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 ? _refine.details ;DISTANCES AND ANGLES WITHIN THE BASES WERE RESTRAINED TO TARGET VALUES. ALL OTHER CHEMICALLY EQUIVALENT BOND DISTANCES WERE RESTRAINED TO BE SIMILAR BY SAME DISTANCE RESTRAINTS. SIGMAS FOR BOTH TARGET AND SIMILAR DISTANCE RESTRAINTS WERE SET AT 0.030 ANGSTROMS FOR BONDS AND 0.050 ANGSTROMS FOR ANGLES. SADI_* 0.15 C3'_- P C3'_1 P_2 SADI_* 0.15 C5' P C5'_2 P_2 ISOR 0.1 ISOR 0.05 C2_3 C2_5 ISOR 0.025 C15B_41 DELU C15B_41 O10B_41 C14_41 C10_41 C20_ 41 DELU O5'_21 C5'_21 C4'_21 C3'_21 C2'_21 C1'_21 O4'_21 BUMP ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 245D _refine_analyze.Luzzati_coordinate_error_obs 0.20 _refine_analyze.Luzzati_sigma_a_obs 0.17 _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 ? _refine_analyze.occupancy_sum_non_hydrogen ? _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 240 _refine_hist.pdbx_number_atoms_ligand 115 _refine_hist.number_atoms_solvent 66 _refine_hist.number_atoms_total 421 _refine_hist.d_res_high 1.400 _refine_hist.d_res_low 8.000 # 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 0.026 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 245D _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.1600000 _pdbx_refine.free_R_factor_no_cutoff 0.2520000 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 245D _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 245D _struct.title ;DNA-DRUG REFINEMENT: A COMPARISON OF THE PROGRAMS NUCLSQ, PROLSQ, SHELXL93 AND X-PLOR, USING THE LOW TEMPERATURE D(TGATCA)-NOGALAMYCIN STRUCTURE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 245D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 245D _struct_ref.pdbx_db_accession 245D _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 245D A 1 ? 6 ? 245D 1 ? 6 ? 1 6 2 1 245D B 1 ? 6 ? 245D 7 ? 12 ? 7 12 # _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 # _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 # 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 DT 1 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 1 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 1 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 3 B DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 3 B DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 4 B DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 4 B DA 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 ? ? A DA 6 N1 ? ? ? 1_555 B DT 1 N3 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 1 O4 ? ? A DA 6 B DT 7 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 B NGM 13 ? 16 'BINDING SITE FOR RESIDUE NGM B 13' AC2 Software A NGM 14 ? 13 'BINDING SITE FOR RESIDUE NGM A 14' 'DRUG BINDING SITE' ? ? ? ? ? ? ? # 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 16 DT A 1 ? DT A 1 . ? 6_555 ? 2 AC1 16 DC A 5 ? DC A 5 . ? 1_555 ? 3 AC1 16 DA A 6 ? DA A 6 . ? 1_555 ? 4 AC1 16 DA A 6 ? DA A 6 . ? 3_545 ? 5 AC1 16 HOH E . ? HOH A 21 . ? 1_555 ? 6 AC1 16 HOH E . ? HOH A 35 . ? 6_555 ? 7 AC1 16 DT B 1 ? DT B 7 . ? 1_555 ? 8 AC1 16 DG B 2 ? DG B 8 . ? 1_555 ? 9 AC1 16 DA B 3 ? DA B 9 . ? 1_555 ? 10 AC1 16 DT B 4 ? DT B 10 . ? 1_555 ? 11 AC1 16 HOH F . ? HOH B 15 . ? 1_555 ? 12 AC1 16 HOH F . ? HOH B 23 . ? 1_555 ? 13 AC1 16 HOH F . ? HOH B 28 . ? 1_555 ? 14 AC1 16 HOH F . ? HOH B 39 . ? 1_555 ? 15 AC1 16 HOH F . ? HOH B 41 . ? 1_555 ? 16 AC1 16 HOH F . ? HOH B 70 . ? 1_555 ? 17 AC2 13 DT A 1 ? DT A 1 . ? 1_555 ? 18 AC2 13 DG A 2 ? DG A 2 . ? 1_555 ? 19 AC2 13 DA A 3 ? DA A 3 . ? 1_555 ? 20 AC2 13 DT A 4 ? DT A 4 . ? 1_555 ? 21 AC2 13 HOH E . ? HOH A 19 . ? 1_555 ? 22 AC2 13 HOH E . ? HOH A 32 . ? 1_555 ? 23 AC2 13 HOH E . ? HOH A 33 . ? 1_555 ? 24 AC2 13 HOH E . ? HOH A 54 . ? 1_555 ? 25 AC2 13 HOH E . ? HOH A 66 . ? 1_555 ? 26 AC2 13 HOH E . ? HOH A 78 . ? 1_555 ? 27 AC2 13 DC B 5 ? DC B 11 . ? 1_555 ? 28 AC2 13 DA B 6 ? DA B 12 . ? 1_555 ? 29 AC2 13 HOH F . ? HOH B 38 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C2'" A DT 1 ? ? "C1'" A DT 1 ? ? 1.581 1.519 0.062 0.010 N 2 1 "C2'" A DG 2 ? ? "C1'" A DG 2 ? ? 1.607 1.519 0.088 0.010 N 3 1 "C2'" A DC 5 ? ? "C1'" A DC 5 ? ? 1.586 1.519 0.067 0.010 N 4 1 C5 B DT 7 ? ? C7 B DT 7 ? ? 1.532 1.496 0.036 0.006 N 5 1 "C2'" B DG 8 ? ? "C1'" B DG 8 ? ? 1.607 1.519 0.088 0.010 N 6 1 "C2'" B DC 11 ? ? "C1'" B DC 11 ? ? 1.588 1.519 0.069 0.010 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DT 1 ? ? "C4'" A DT 1 ? ? "C3'" A DT 1 ? ? 101.89 104.50 -2.61 0.40 N 2 1 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.18 108.30 1.88 0.30 N 3 1 N1 A DT 1 ? ? C2 A DT 1 ? ? N3 A DT 1 ? ? 110.87 114.60 -3.73 0.60 N 4 1 "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? "C2'" A DG 2 ? ? 110.22 103.10 7.12 0.90 N 5 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 120.27 108.30 11.97 0.30 N 6 1 C2 A DG 2 ? ? N3 A DG 2 ? ? C4 A DG 2 ? ? 108.45 111.90 -3.45 0.50 N 7 1 "C3'" A DG 2 ? ? "O3'" A DG 2 ? ? P A DA 3 ? ? 135.22 119.70 15.52 1.20 Y 8 1 N3 A DT 4 ? ? C2 A DT 4 ? ? O2 A DT 4 ? ? 118.03 122.30 -4.27 0.60 N 9 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 120.21 108.30 11.91 0.30 N 10 1 C2 A DC 5 ? ? N3 A DC 5 ? ? C4 A DC 5 ? ? 123.10 119.90 3.20 0.50 N 11 1 "C4'" B DT 7 ? ? "C3'" B DT 7 ? ? "C2'" B DT 7 ? ? 109.56 103.10 6.46 0.90 N 12 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 111.17 108.30 2.87 0.30 N 13 1 "C3'" B DG 8 ? ? "C2'" B DG 8 ? ? "C1'" B DG 8 ? ? 97.45 102.40 -4.95 0.80 N 14 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 120.27 108.30 11.97 0.30 N 15 1 OP1 B DA 9 ? ? P B DA 9 ? ? OP2 B DA 9 ? ? 107.35 119.60 -12.25 1.50 N 16 1 "C4'" B DA 9 ? ? "C3'" B DA 9 ? ? "C2'" B DA 9 ? ? 108.55 103.10 5.45 0.90 N 17 1 "O4'" B DA 9 ? ? "C1'" B DA 9 ? ? N9 B DA 9 ? ? 111.13 108.30 2.83 0.30 N 18 1 "C4'" B DT 10 ? ? "C3'" B DT 10 ? ? "C2'" B DT 10 ? ? 108.95 103.10 5.85 0.90 N 19 1 C2 B DT 10 ? ? N3 B DT 10 ? ? C4 B DT 10 ? ? 133.25 127.20 6.05 0.60 N 20 1 N3 B DT 10 ? ? C4 B DT 10 ? ? C5 B DT 10 ? ? 111.45 115.20 -3.75 0.60 N 21 1 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 117.43 108.30 9.13 0.30 N # _struct_site_keywords.site_id 'DRUG BINDING SITE' _struct_site_keywords.text INTERCALATION # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 77 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 NGM C1 C Y N 147 NGM C2 C Y N 148 NGM C3 C Y N 149 NGM C4 C Y N 150 NGM C5 C N N 151 NGM C6 C Y N 152 NGM C7 C N S 153 NGM C8 C N N 154 NGM C9 C N S 155 NGM C10 C N R 156 NGM C11 C Y N 157 NGM C12 C N N 158 NGM C13 C N N 159 NGM C14 C N N 160 NGM C15 C N N 161 NGM C16 C Y N 162 NGM C17 C Y N 163 NGM C18 C Y N 164 NGM C19 C Y N 165 NGM C20 C Y N 166 NGM C21 C Y N 167 NGM C22 C N N 168 NGM C23 C N N 169 NGM C24 C N N 170 NGM C25 C N N 171 NGM C26 C N N 172 NGM C27 C N N 173 NGM C28 C N N 174 NGM C29 C N N 175 NGM C30 C N S 176 NGM C31 C N S 177 NGM C32 C N R 178 NGM C33 C N R 179 NGM C34 C N R 180 NGM "C1'" C N R 181 NGM "C2'" C N R 182 NGM "C3'" C N R 183 NGM "C4'" C N S 184 NGM "C5'" C N S 185 NGM N1 N N N 186 NGM O1 O N N 187 NGM O2 O N N 188 NGM O4 O N N 189 NGM O5 O N N 190 NGM O6 O N N 191 NGM O7 O N N 192 NGM O9 O N N 193 NGM O10 O N N 194 NGM O14 O N N 195 NGM O12 O N N 196 NGM O15 O N N 197 NGM O16 O N N 198 NGM "O1'" O N N 199 NGM "O2'" O N N 200 NGM "O3'" O N N 201 NGM "O4'" O N N 202 NGM H3 H N N 203 NGM H7 H N N 204 NGM H81 H N N 205 NGM H82 H N N 206 NGM H10 H N N 207 NGM H11 H N N 208 NGM H131 H N N 209 NGM H132 H N N 210 NGM H133 H N N 211 NGM H151 H N N 212 NGM H152 H N N 213 NGM H153 H N N 214 NGM H221 H N N 215 NGM H222 H N N 216 NGM H223 H N N 217 NGM H231 H N N 218 NGM H232 H N N 219 NGM H233 H N N 220 NGM H241 H N N 221 NGM H242 H N N 222 NGM H243 H N N 223 NGM H251 H N N 224 NGM H252 H N N 225 NGM H253 H N N 226 NGM H261 H N N 227 NGM H262 H N N 228 NGM H263 H N N 229 NGM H271 H N N 230 NGM H272 H N N 231 NGM H273 H N N 232 NGM H281 H N N 233 NGM H282 H N N 234 NGM H283 H N N 235 NGM H291 H N N 236 NGM H292 H N N 237 NGM H293 H N N 238 NGM H30 H N N 239 NGM H31 H N N 240 NGM H32 H N N 241 NGM H33 H N N 242 NGM "H1'" H N N 243 NGM "H2'" H N N 244 NGM "H4'" H N N 245 NGM "H5'" H N N 246 NGM HO4 H N N 247 NGM HO6 H N N 248 NGM HO9 H N N 249 NGM H15 H N N 250 NGM H16 H N N 251 # 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 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 NGM C1 C2 doub Y N 152 NGM C1 C16 sing Y N 153 NGM C1 O1 sing N N 154 NGM C2 C3 sing Y N 155 NGM C2 C34 sing N N 156 NGM C3 C4 doub Y N 157 NGM C3 H3 sing N N 158 NGM C4 C17 sing Y N 159 NGM C4 O4 sing N N 160 NGM C5 C17 sing N N 161 NGM C5 C18 sing N N 162 NGM C5 O5 doub N N 163 NGM C6 C18 doub Y N 164 NGM C6 C19 sing Y N 165 NGM C6 O6 sing N N 166 NGM C7 C8 sing N N 167 NGM C7 C19 sing N N 168 NGM C7 O7 sing N N 169 NGM C7 H7 sing N N 170 NGM C8 C9 sing N N 171 NGM C8 H81 sing N N 172 NGM C8 H82 sing N N 173 NGM C9 C10 sing N N 174 NGM C9 C13 sing N N 175 NGM C9 O9 sing N N 176 NGM C10 C14 sing N N 177 NGM C10 C20 sing N N 178 NGM C10 H10 sing N N 179 NGM C11 C20 sing Y N 180 NGM C11 C21 doub Y N 181 NGM C11 H11 sing N N 182 NGM C12 C16 sing N N 183 NGM C12 C21 sing N N 184 NGM C12 O12 doub N N 185 NGM C13 H131 sing N N 186 NGM C13 H132 sing N N 187 NGM C13 H133 sing N N 188 NGM C14 O10 sing N N 189 NGM C14 O14 doub N N 190 NGM C15 O10 sing N N 191 NGM C15 H151 sing N N 192 NGM C15 H152 sing N N 193 NGM C15 H153 sing N N 194 NGM C16 C17 doub Y N 195 NGM C18 C21 sing Y N 196 NGM C19 C20 doub Y N 197 NGM C22 C34 sing N N 198 NGM C22 H221 sing N N 199 NGM C22 H222 sing N N 200 NGM C22 H223 sing N N 201 NGM C23 N1 sing N N 202 NGM C23 H231 sing N N 203 NGM C23 H232 sing N N 204 NGM C23 H233 sing N N 205 NGM C24 N1 sing N N 206 NGM C24 H241 sing N N 207 NGM C24 H242 sing N N 208 NGM C24 H243 sing N N 209 NGM C25 "C5'" sing N N 210 NGM C25 H251 sing N N 211 NGM C25 H252 sing N N 212 NGM C25 H253 sing N N 213 NGM C26 "O4'" sing N N 214 NGM C26 H261 sing N N 215 NGM C26 H262 sing N N 216 NGM C26 H263 sing N N 217 NGM C27 "O3'" sing N N 218 NGM C27 H271 sing N N 219 NGM C27 H272 sing N N 220 NGM C27 H273 sing N N 221 NGM C28 "C3'" sing N N 222 NGM C28 H281 sing N N 223 NGM C28 H282 sing N N 224 NGM C28 H283 sing N N 225 NGM C29 "O2'" sing N N 226 NGM C29 H291 sing N N 227 NGM C29 H292 sing N N 228 NGM C29 H293 sing N N 229 NGM C30 C31 sing N N 230 NGM C30 O1 sing N N 231 NGM C30 O2 sing N N 232 NGM C30 H30 sing N N 233 NGM C31 C32 sing N N 234 NGM C31 O15 sing N N 235 NGM C31 H31 sing N N 236 NGM C32 C33 sing N N 237 NGM C32 N1 sing N N 238 NGM C32 H32 sing N N 239 NGM C33 C34 sing N N 240 NGM C33 O16 sing N N 241 NGM C33 H33 sing N N 242 NGM C34 O2 sing N N 243 NGM "C1'" "C2'" sing N N 244 NGM "C1'" O7 sing N N 245 NGM "C1'" "O1'" sing N N 246 NGM "C1'" "H1'" sing N N 247 NGM "C2'" "C3'" sing N N 248 NGM "C2'" "O2'" sing N N 249 NGM "C2'" "H2'" sing N N 250 NGM "C3'" "C4'" sing N N 251 NGM "C3'" "O3'" sing N N 252 NGM "C4'" "C5'" sing N N 253 NGM "C4'" "O4'" sing N N 254 NGM "C4'" "H4'" sing N N 255 NGM "C5'" "O1'" sing N N 256 NGM "C5'" "H5'" sing N N 257 NGM O4 HO4 sing N N 258 NGM O6 HO6 sing N N 259 NGM O9 HO9 sing N N 260 NGM O15 H15 sing N N 261 NGM O16 H16 sing N N 262 # _ndb_struct_conf_na.entry_id 245D _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 DT 1 1_555 B DA 6 1_555 0.051 -0.022 -0.011 11.805 2.633 -0.068 1 A_DT1:DA12_B A 1 ? B 12 ? 20 1 1 A DG 2 1_555 B DC 5 1_555 -0.399 -0.035 -0.437 -25.631 2.270 -0.617 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DA 3 1_555 B DT 4 1_555 -0.058 0.063 -0.116 -5.805 -3.796 5.149 3 A_DA3:DT10_B A 3 ? B 10 ? 20 1 1 A DT 4 1_555 B DA 3 1_555 -0.006 -0.015 -0.110 6.038 -3.616 5.154 4 A_DT4:DA9_B A 4 ? B 9 ? 20 1 1 A DC 5 1_555 B DG 2 1_555 0.362 -0.030 -0.493 24.974 2.491 -0.753 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DA 6 1_555 B DT 1 1_555 0.062 -0.038 -0.047 -10.955 1.374 -1.577 6 A_DA6:DT7_B A 6 ? B 7 ? 20 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 DT 1 1_555 B DA 6 1_555 A DG 2 1_555 B DC 5 1_555 1.531 -0.150 7.148 12.798 1.588 29.661 -0.915 2.440 7.167 2.934 -23.642 32.286 1 AA_DT1DG2:DC11DA12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 5 1_555 A DA 3 1_555 B DT 4 1_555 -0.404 0.474 3.102 -2.930 4.975 30.441 -0.040 0.211 3.162 9.368 5.518 30.971 2 AA_DG2DA3:DT10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DA 3 1_555 B DT 4 1_555 A DT 4 1_555 B DA 3 1_555 0.189 -0.593 3.138 0.342 -6.361 33.371 -0.020 -0.270 3.195 -10.954 -0.589 33.956 3 AA_DA3DT4:DA9DT10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DT 4 1_555 B DA 3 1_555 A DC 5 1_555 B DG 2 1_555 0.473 0.619 3.118 5.507 5.462 30.698 0.142 0.133 3.212 10.115 -10.200 31.640 4 AA_DT4DC5:DG8DA9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B DG 2 1_555 A DA 6 1_555 B DT 1 1_555 -1.321 0.371 7.126 -12.843 0.361 33.769 0.484 -1.979 7.147 0.595 21.181 36.064 5 AA_DC5DA6:DT7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _atom_sites.entry_id 245D _atom_sites.fract_transf_matrix[1][1] 0.026817 _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] 0.026817 _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] 0.014061 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_