data_1VTH # _entry.id 1VTH # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 1VTH pdb_00001vth 10.2210/pdb1vth/pdb NDB DDF031 ? ? RCSB RCSB003041 ? ? WWPDB D_1000003041 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-07-13 2 'Structure model' 1 1 2023-12-27 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1VTH _pdbx_database_status.recvd_initial_deposition_date 1992-03-01 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _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 'Nunn, C.M.' 1 'Van Meervelt, L.' 2 'Zhang, S.' 3 'Moore, M.H.' 4 'Kennard, O.' 5 # 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 Interactions: The Crystal Structures of d(TGTACA) and d(TGATCA) Complexed with Daunomycin' J.Mol.Biol. 222 167 177 1991 JMOBAK UK 0022-2836 0070 ? ? ? 1 'DNA-Drug Interactions: The Crystal Structure of d(CGATCG) Complexed with Daunomycin' J.Mol.Biol. 206 693 705 1989 JMOBAK UK 0022-2836 0070 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nunn, C.M.' 1 ? primary 'Van Meervelt, L.' 2 ? primary 'Zhang, S.' 3 ? primary 'Moore, M.H.' 4 ? primary 'Kennard, O.' 5 ? 1 'Moore, M.H.' 6 ? 1 'Hunter, W.N.' 7 ? 1 ;D'Estaintot, B.L. ; 8 ? 1 'Kennard, O.' 9 ? # 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*TP*AP*CP*A)-3') ; 1808.229 1 ? ? ? ? 2 non-polymer syn DAUNOMYCIN 527.520 1 ? ? ? ? 3 water nat water 18.015 44 ? ? ? ? # _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)(DT)(DA)(DC)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TGTACA _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 DAUNOMYCIN DM1 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 DT n 1 4 DA 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 DM1 non-polymer . DAUNOMYCIN DAUNORUBICIN 'C27 H29 N O10' 527.520 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 DT 1 1 1 DT T A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DA 6 6 6 DA A A . 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 B 2 DM1 1 7 7 DM1 DM1 A . C 3 HOH 1 8 8 HOH HOH A . C 3 HOH 2 9 9 HOH HOH A . C 3 HOH 3 10 10 HOH HOH A . C 3 HOH 4 11 11 HOH HOH A . C 3 HOH 5 12 12 HOH HOH A . C 3 HOH 6 13 13 HOH HOH A . C 3 HOH 7 14 14 HOH HOH A . C 3 HOH 8 15 15 HOH HOH A . C 3 HOH 9 16 16 HOH HOH A . C 3 HOH 10 17 17 HOH HOH A . C 3 HOH 11 18 18 HOH HOH A . C 3 HOH 12 19 19 HOH HOH A . C 3 HOH 13 20 20 HOH HOH A . C 3 HOH 14 21 21 HOH HOH A . C 3 HOH 15 22 22 HOH HOH A . C 3 HOH 16 23 23 HOH HOH A . C 3 HOH 17 24 24 HOH HOH A . C 3 HOH 18 25 25 HOH HOH A . C 3 HOH 19 26 26 HOH HOH A . C 3 HOH 20 27 27 HOH HOH A . C 3 HOH 21 28 28 HOH HOH A . C 3 HOH 22 29 29 HOH HOH A . C 3 HOH 23 30 30 HOH HOH A . C 3 HOH 24 31 31 HOH HOH A . C 3 HOH 25 32 32 HOH HOH A . C 3 HOH 26 33 33 HOH HOH A . C 3 HOH 27 34 34 HOH HOH A . C 3 HOH 28 35 35 HOH HOH A . C 3 HOH 29 36 36 HOH HOH A . C 3 HOH 30 37 37 HOH HOH A . C 3 HOH 31 38 38 HOH HOH A . C 3 HOH 32 39 39 HOH HOH A . C 3 HOH 33 40 40 HOH HOH A . C 3 HOH 34 41 41 HOH HOH A . C 3 HOH 35 42 42 HOH HOH A . C 3 HOH 36 43 43 HOH HOH A . C 3 HOH 37 44 44 HOH HOH A . C 3 HOH 38 45 45 HOH HOH A . C 3 HOH 39 46 46 HOH HOH A . C 3 HOH 40 47 47 HOH HOH A . C 3 HOH 41 48 48 HOH HOH A . C 3 HOH 42 49 49 HOH HOH A . C 3 HOH 43 50 50 HOH HOH A . C 3 HOH 44 51 51 HOH HOH A . # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1VTH _cell.length_a 28.020 _cell.length_b 28.020 _cell.length_c 52.710 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 1VTH _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 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1VTH _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 57.00 _exptl_crystal.density_Matthews 2.86 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 293.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.50 _exptl_crystal_grow.pdbx_details 'pH 6.50, VAPOR DIFFUSION, temperature 293.00K' _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 3 1 2 1 MPD 4 5 6 1 3 1 'MG ACETATE' 7 8 9 1 4 1 SPERMINE_HCL 10 11 12 1 5 1 'NA CACODYLATE' 13 14 15 1 6 2 WATER 16 17 18 1 7 2 MPD 19 20 21 # _diffrn.id 1 _diffrn.ambient_temp 275.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'SYNTEX P21' _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 '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 ? _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1VTH _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 1.500 _reflns.number_obs 4852 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _refine.entry_id 1VTH _refine.ls_number_reflns_obs 1811 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 3.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 1.600 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.2500000 _refine.ls_R_factor_all ? _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 ? _refine.ls_number_restraints ? _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 ? _refine.details ? _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_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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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_ESU_R ? _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 120 _refine_hist.pdbx_number_atoms_ligand 38 _refine_hist.number_atoms_solvent 44 _refine_hist.number_atoms_total 202 _refine_hist.d_res_high 1.600 _refine_hist.d_res_low 10.000 # _database_PDB_matrix.entry_id 1VTH _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 1VTH _struct.title 'DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURES OF D(TGTACA) COMPLEXED WITH DAUNOMYCIN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1VTH _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 2 ? C N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 1VTH _struct_ref.pdbx_db_accession 1VTH _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1VTH _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1VTH _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 8_665 -y+1,-x+1,-z+1/2 0.0000000000 -1.0000000000 0.0000000000 28.0200000000 -1.0000000000 0.0000000000 0.0000000000 28.0200000000 0.0000000000 0.0000000000 -1.0000000000 26.3550000000 # _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 DT 1 N3 ? ? ? 1_555 A DA 6 N1 ? ? A DT 1 A DA 6 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 A DA 6 N6 ? ? A DT 1 A DA 6 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 2 A DC 5 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 2 A DC 5 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 2 A DC 5 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 3 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 3 A DA 4 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 3 A DA 4 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 3 N3 ? ? A DA 4 A DT 3 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 3 O4 ? ? A DA 4 A DT 3 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 2 N1 ? ? A DC 5 A DG 2 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 2 O6 ? ? A DC 5 A DG 2 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 2 N2 ? ? A DC 5 A DG 2 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 A DT 1 N3 ? ? A DA 6 A DT 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 A DT 1 O4 ? ? A DA 6 A DT 1 8_665 ? ? ? ? ? ? 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 DM1 7 ? 10 'BINDING SITE FOR RESIDUE DM1 A 7' 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 10 DT A 1 ? DT A 1 . ? 8_665 ? 2 AC1 10 DG A 2 ? DG A 2 . ? 8_665 ? 3 AC1 10 DT A 3 ? DT A 3 . ? 8_665 ? 4 AC1 10 DC A 5 ? DC A 5 . ? 1_555 ? 5 AC1 10 DA A 6 ? DA A 6 . ? 1_555 ? 6 AC1 10 HOH C . ? HOH A 15 . ? 1_555 ? 7 AC1 10 HOH C . ? HOH A 20 . ? 8_665 ? 8 AC1 10 HOH C . ? HOH A 22 . ? 1_555 ? 9 AC1 10 HOH C . ? HOH A 36 . ? 8_665 ? 10 AC1 10 HOH C . ? HOH A 40 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 15 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 51 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.09 # 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 "C5'" A DT 1 ? ? "C4'" A DT 1 ? ? 1.599 1.512 0.087 0.007 N 2 1 N3 A DT 1 ? ? C4 A DT 1 ? ? 1.314 1.382 -0.068 0.008 N 3 1 C4 A DT 1 ? ? C5 A DT 1 ? ? 1.366 1.445 -0.079 0.009 N 4 1 C5 A DT 1 ? ? C6 A DT 1 ? ? 1.262 1.339 -0.077 0.007 N 5 1 C4 A DT 1 ? ? O4 A DT 1 ? ? 1.290 1.228 0.062 0.009 N 6 1 P A DG 2 ? ? OP2 A DG 2 ? ? 1.603 1.485 0.118 0.017 N 7 1 "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 1.594 1.529 0.065 0.010 N 8 1 "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.383 1.446 -0.063 0.010 N 9 1 N1 A DG 2 ? ? C2 A DG 2 ? ? 1.261 1.373 -0.112 0.008 N 10 1 N3 A DG 2 ? ? C4 A DG 2 ? ? 1.396 1.350 0.046 0.007 N 11 1 C4 A DG 2 ? ? C5 A DG 2 ? ? 1.422 1.379 0.043 0.007 N 12 1 C5 A DG 2 ? ? N7 A DG 2 ? ? 1.465 1.388 0.077 0.006 N 13 1 N9 A DG 2 ? ? C4 A DG 2 ? ? 1.436 1.375 0.061 0.008 N 14 1 C2 A DG 2 ? ? N2 A DG 2 ? ? 1.267 1.341 -0.074 0.010 N 15 1 C2 A DT 3 ? ? N3 A DT 3 ? ? 1.425 1.373 0.052 0.008 N 16 1 N3 A DT 3 ? ? C4 A DT 3 ? ? 1.243 1.382 -0.139 0.008 N 17 1 C4 A DT 3 ? ? C5 A DT 3 ? ? 1.356 1.445 -0.089 0.009 N 18 1 C2 A DT 3 ? ? O2 A DT 3 ? ? 1.360 1.220 0.140 0.008 N 19 1 P A DA 4 ? ? OP2 A DA 4 ? ? 1.613 1.485 0.128 0.017 N 20 1 P A DA 4 ? ? "O5'" A DA 4 ? ? 1.506 1.593 -0.087 0.010 N 21 1 "O3'" A DA 4 ? ? "C3'" A DA 4 ? ? 1.377 1.419 -0.042 0.006 N 22 1 N1 A DA 4 ? ? C2 A DA 4 ? ? 1.283 1.339 -0.056 0.009 N 23 1 N3 A DA 4 ? ? C4 A DA 4 ? ? 1.303 1.344 -0.041 0.006 N 24 1 "C2'" A DC 5 ? ? "C1'" A DC 5 ? ? 1.607 1.519 0.088 0.010 N 25 1 C2 A DC 5 ? ? O2 A DC 5 ? ? 1.322 1.240 0.082 0.009 N 26 1 C5 A DC 5 ? ? C6 A DC 5 ? ? 1.401 1.339 0.062 0.008 N 27 1 "O3'" A DA 6 ? ? "C3'" A DA 6 ? ? 1.381 1.419 -0.038 0.006 N 28 1 N9 A DA 6 ? ? C4 A DA 6 ? ? 1.338 1.374 -0.036 0.006 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 DT 1 ? ? "C5'" A DT 1 ? ? "C4'" A DT 1 ? ? 98.20 109.40 -11.20 0.80 N 2 1 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? "C2'" A DT 1 ? ? 99.88 105.90 -6.02 0.80 N 3 1 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 113.14 108.30 4.84 0.30 N 4 1 N3 A DT 1 ? ? C4 A DT 1 ? ? C5 A DT 1 ? ? 120.27 115.20 5.07 0.60 N 5 1 N3 A DT 1 ? ? C2 A DT 1 ? ? O2 A DT 1 ? ? 126.72 122.30 4.42 0.60 N 6 1 N3 A DT 1 ? ? C4 A DT 1 ? ? O4 A DT 1 ? ? 116.08 119.90 -3.82 0.60 N 7 1 "O3'" A DT 1 ? ? P A DG 2 ? ? OP1 A DG 2 ? ? 89.12 105.20 -16.08 2.20 Y 8 1 "O5'" A DG 2 ? ? P A DG 2 ? ? OP2 A DG 2 ? ? 120.29 110.70 9.59 1.20 N 9 1 P A DG 2 ? ? "O5'" A DG 2 ? ? "C5'" A DG 2 ? ? 103.57 120.90 -17.33 1.60 N 10 1 "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 116.03 106.00 10.03 0.60 N 11 1 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 102.64 114.10 -11.46 1.80 N 12 1 "C1'" A DG 2 ? ? "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 101.19 110.10 -8.91 1.00 N 13 1 "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? "C2'" A DG 2 ? ? 96.15 102.20 -6.05 0.70 N 14 1 C6 A DG 2 ? ? N1 A DG 2 ? ? C2 A DG 2 ? ? 136.93 125.10 11.83 0.60 N 15 1 C2 A DG 2 ? ? N3 A DG 2 ? ? C4 A DG 2 ? ? 108.08 111.90 -3.82 0.50 N 16 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 104.38 111.50 -7.12 0.50 N 17 1 C4 A DG 2 ? ? C5 A DG 2 ? ? N7 A DG 2 ? ? 114.93 110.80 4.13 0.40 N 18 1 C5 A DG 2 ? ? N7 A DG 2 ? ? C8 A DG 2 ? ? 96.71 104.30 -7.59 0.50 N 19 1 N7 A DG 2 ? ? C8 A DG 2 ? ? N9 A DG 2 ? ? 121.81 113.10 8.71 0.50 N 20 1 N9 A DG 2 ? ? C4 A DG 2 ? ? C5 A DG 2 ? ? 101.01 105.40 -4.39 0.40 N 21 1 N3 A DG 2 ? ? C4 A DG 2 ? ? N9 A DG 2 ? ? 129.92 126.00 3.92 0.60 N 22 1 N1 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 137.50 119.90 17.60 0.60 N 23 1 C5 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 117.99 128.60 -10.61 0.60 N 24 1 C8 A DG 2 ? ? N9 A DG 2 ? ? "C1'" A DG 2 ? ? 136.93 127.00 9.93 1.30 N 25 1 C4 A DG 2 ? ? N9 A DG 2 ? ? "C1'" A DG 2 ? ? 117.54 126.50 -8.96 1.30 N 26 1 "C3'" A DG 2 ? ? "O3'" A DG 2 ? ? P A DT 3 ? ? 136.30 119.70 16.60 1.20 Y 27 1 OP1 A DT 3 ? ? P A DT 3 ? ? OP2 A DT 3 ? ? 129.81 119.60 10.21 1.50 N 28 1 "O5'" A DT 3 ? ? "C5'" A DT 3 ? ? "C4'" A DT 3 ? ? 102.10 109.40 -7.30 0.80 N 29 1 P A DT 3 ? ? "O5'" A DT 3 ? ? "C5'" A DT 3 ? ? 109.41 120.90 -11.49 1.60 N 30 1 "C5'" A DT 3 ? ? "C4'" A DT 3 ? ? "O4'" A DT 3 ? ? 116.51 109.80 6.71 1.10 N 31 1 N1 A DT 3 ? ? "C1'" A DT 3 ? ? "C2'" A DT 3 ? ? 101.12 112.60 -11.48 1.90 N 32 1 C6 A DT 3 ? ? N1 A DT 3 ? ? C2 A DT 3 ? ? 114.47 121.30 -6.83 0.50 N 33 1 C2 A DT 3 ? ? N3 A DT 3 ? ? C4 A DT 3 ? ? 120.86 127.20 -6.34 0.60 N 34 1 N3 A DT 3 ? ? C4 A DT 3 ? ? C5 A DT 3 ? ? 123.05 115.20 7.85 0.60 N 35 1 N1 A DT 3 ? ? C2 A DT 3 ? ? O2 A DT 3 ? ? 114.22 123.10 -8.88 0.80 N 36 1 N3 A DT 3 ? ? C2 A DT 3 ? ? O2 A DT 3 ? ? 127.77 122.30 5.47 0.60 N 37 1 N3 A DT 3 ? ? C4 A DT 3 ? ? O4 A DT 3 ? ? 113.92 119.90 -5.98 0.60 N 38 1 C4 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 129.15 119.00 10.15 0.60 N 39 1 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 114.54 122.90 -8.36 0.60 N 40 1 C6 A DT 3 ? ? N1 A DT 3 ? ? "C1'" A DT 3 ? ? 131.25 120.40 10.85 1.50 N 41 1 "C3'" A DT 3 ? ? "O3'" A DT 3 ? ? P A DA 4 ? ? 146.18 119.70 26.48 1.20 Y 42 1 "O3'" A DT 3 ? ? P A DA 4 ? ? "O5'" A DA 4 ? ? 124.81 104.00 20.81 1.90 Y 43 1 "O3'" A DT 3 ? ? P A DA 4 ? ? OP2 A DA 4 ? ? 91.77 105.20 -13.43 2.20 Y 44 1 OP1 A DA 4 ? ? P A DA 4 ? ? OP2 A DA 4 ? ? 101.09 119.60 -18.51 1.50 N 45 1 "O4'" A DA 4 ? ? "C4'" A DA 4 ? ? "C3'" A DA 4 ? ? 111.33 106.00 5.33 0.60 N 46 1 "C5'" A DA 4 ? ? "C4'" A DA 4 ? ? "O4'" A DA 4 ? ? 116.45 109.80 6.65 1.10 N 47 1 "C1'" A DA 4 ? ? "O4'" A DA 4 ? ? "C4'" A DA 4 ? ? 103.22 110.10 -6.88 1.00 N 48 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? "C2'" A DA 4 ? ? 111.41 106.80 4.61 0.50 N 49 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 94.88 108.00 -13.12 0.70 N 50 1 N9 A DA 4 ? ? C4 A DA 4 ? ? C5 A DA 4 ? ? 103.34 105.80 -2.46 0.40 N 51 1 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 124.74 118.60 6.14 0.60 N 52 1 "C3'" A DA 4 ? ? "O3'" A DA 4 ? ? P A DC 5 ? ? 129.47 119.70 9.77 1.20 Y 53 1 "O3'" A DA 4 ? ? P A DC 5 ? ? OP2 A DC 5 ? ? 128.61 110.50 18.11 1.10 Y 54 1 OP1 A DC 5 ? ? P A DC 5 ? ? OP2 A DC 5 ? ? 92.98 119.60 -26.62 1.50 N 55 1 "O5'" A DC 5 ? ? P A DC 5 ? ? OP1 A DC 5 ? ? 133.68 110.70 22.98 1.20 N 56 1 "O5'" A DC 5 ? ? P A DC 5 ? ? OP2 A DC 5 ? ? 91.30 105.70 -14.40 0.90 N 57 1 P A DC 5 ? ? "O5'" A DC 5 ? ? "C5'" A DC 5 ? ? 106.62 120.90 -14.28 1.60 N 58 1 "C5'" A DC 5 ? ? "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? 127.76 115.70 12.06 1.20 N 59 1 "C5'" A DC 5 ? ? "C4'" A DC 5 ? ? "O4'" A DC 5 ? ? 84.97 109.30 -24.33 1.90 N 60 1 "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? "C1'" A DC 5 ? ? 94.13 102.40 -8.27 0.80 N 61 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? "C2'" A DC 5 ? ? 94.07 105.90 -11.83 0.80 N 62 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 110.55 108.30 2.25 0.30 N 63 1 C4 A DC 5 ? ? C5 A DC 5 ? ? C6 A DC 5 ? ? 112.37 117.40 -5.03 0.50 N 64 1 N3 A DC 5 ? ? C4 A DC 5 ? ? N4 A DC 5 ? ? 126.47 118.00 8.47 0.70 N 65 1 C5 A DC 5 ? ? C4 A DC 5 ? ? N4 A DC 5 ? ? 110.85 120.20 -9.35 0.70 N 66 1 "C3'" A DC 5 ? ? "O3'" A DC 5 ? ? P A DA 6 ? ? 138.21 119.70 18.51 1.20 Y 67 1 "O3'" A DC 5 ? ? P A DA 6 ? ? "O5'" A DA 6 ? ? 116.95 104.00 12.95 1.90 Y 68 1 "O5'" A DA 6 ? ? P A DA 6 ? ? OP1 A DA 6 ? ? 98.14 105.70 -7.56 0.90 N 69 1 P A DA 6 ? ? "O5'" A DA 6 ? ? "C5'" A DA 6 ? ? 110.14 120.90 -10.76 1.60 N 70 1 "O4'" A DA 6 ? ? "C4'" A DA 6 ? ? "C3'" A DA 6 ? ? 101.37 104.50 -3.13 0.40 N 71 1 "C2'" A DA 6 ? ? "C3'" A DA 6 ? ? "O3'" A DA 6 ? ? 91.54 109.40 -17.86 2.50 N 72 1 C6 A DA 6 ? ? N1 A DA 6 ? ? C2 A DA 6 ? ? 123.00 118.60 4.40 0.60 N 73 1 N1 A DA 6 ? ? C2 A DA 6 ? ? N3 A DA 6 ? ? 125.33 129.30 -3.97 0.50 N 74 1 C5 A DA 6 ? ? N7 A DA 6 ? ? C8 A DA 6 ? ? 99.70 103.90 -4.20 0.50 N 75 1 N7 A DA 6 ? ? C8 A DA 6 ? ? N9 A DA 6 ? ? 118.67 113.80 4.87 0.50 N # _pdbx_validate_chiral.id 1 _pdbx_validate_chiral.PDB_model_num 1 _pdbx_validate_chiral.auth_atom_id "C5'" _pdbx_validate_chiral.label_alt_id ? _pdbx_validate_chiral.auth_asym_id A _pdbx_validate_chiral.auth_comp_id DM1 _pdbx_validate_chiral.auth_seq_id 7 _pdbx_validate_chiral.PDB_ins_code ? _pdbx_validate_chiral.details 'WRONG HAND' _pdbx_validate_chiral.omega . # _struct_site_keywords.site_id 1 _struct_site_keywords.text INTERCALATION # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix '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 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 DM1 C1 C Y N 108 DM1 C2 C Y N 109 DM1 C3 C Y N 110 DM1 C4 C Y N 111 DM1 O4 O N N 112 DM1 C5 C Y N 113 DM1 C6 C N N 114 DM1 O6 O N N 115 DM1 C7 C Y N 116 DM1 C8 C Y N 117 DM1 O8 O N N 118 DM1 C9 C Y N 119 DM1 C10 C N S 120 DM1 O10 O N N 121 DM1 C11 C N N 122 DM1 C12 C N S 123 DM1 O12 O N N 124 DM1 C13 C N N 125 DM1 O13 O N N 126 DM1 C14 C N N 127 DM1 C15 C N N 128 DM1 C16 C Y N 129 DM1 C17 C Y N 130 DM1 O17 O N N 131 DM1 C18 C Y N 132 DM1 C19 C N N 133 DM1 O19 O N N 134 DM1 C20 C Y N 135 DM1 C21 C N N 136 DM1 "C1'" C N R 137 DM1 "C2'" C N N 138 DM1 "C3'" C N S 139 DM1 "N3'" N N N 140 DM1 "C4'" C N S 141 DM1 "O4'" O N N 142 DM1 "C5'" C N S 143 DM1 "O5'" O N N 144 DM1 "C6'" C N N 145 DM1 H1 H N N 146 DM1 H2 H N N 147 DM1 H3 H N N 148 DM1 HO8 H N N 149 DM1 H10 H N N 150 DM1 H111 H N N 151 DM1 H112 H N N 152 DM1 HO12 H N N 153 DM1 H141 H N N 154 DM1 H142 H N N 155 DM1 H143 H N N 156 DM1 H151 H N N 157 DM1 H152 H N N 158 DM1 HO17 H N N 159 DM1 H211 H N N 160 DM1 H212 H N N 161 DM1 H213 H N N 162 DM1 "H1'" H N N 163 DM1 "H2'1" H N N 164 DM1 "H2'2" H N N 165 DM1 "H3'" H N N 166 DM1 "HN'1" H N N 167 DM1 "HN'2" H N N 168 DM1 "H4'" H N N 169 DM1 "HO4'" H N N 170 DM1 "H5'" H N N 171 DM1 "H6'1" H N N 172 DM1 "H6'2" H N N 173 DM1 "H6'3" H N N 174 DT OP3 O N N 175 DT P P N N 176 DT OP1 O N N 177 DT OP2 O N N 178 DT "O5'" O N N 179 DT "C5'" C N N 180 DT "C4'" C N R 181 DT "O4'" O N N 182 DT "C3'" C N S 183 DT "O3'" O N N 184 DT "C2'" C N N 185 DT "C1'" C N R 186 DT N1 N N N 187 DT C2 C N N 188 DT O2 O N N 189 DT N3 N N N 190 DT C4 C N N 191 DT O4 O N N 192 DT C5 C N N 193 DT C7 C N N 194 DT C6 C N N 195 DT HOP3 H N N 196 DT HOP2 H N N 197 DT "H5'" H N N 198 DT "H5''" H N N 199 DT "H4'" H N N 200 DT "H3'" H N N 201 DT "HO3'" H N N 202 DT "H2'" H N N 203 DT "H2''" H N N 204 DT "H1'" H N N 205 DT H3 H N N 206 DT H71 H N N 207 DT H72 H N N 208 DT H73 H N N 209 DT H6 H N N 210 HOH O O N N 211 HOH H1 H N N 212 HOH H2 H N N 213 # 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 DM1 C1 C2 doub Y N 113 DM1 C1 C20 sing Y N 114 DM1 C1 H1 sing N N 115 DM1 C2 C3 sing Y N 116 DM1 C2 H2 sing N N 117 DM1 C3 C4 doub Y N 118 DM1 C3 H3 sing N N 119 DM1 C4 O4 sing N N 120 DM1 C4 C5 sing Y N 121 DM1 O4 C21 sing N N 122 DM1 C5 C6 sing N N 123 DM1 C5 C20 doub Y N 124 DM1 C6 O6 doub N N 125 DM1 C6 C7 sing N N 126 DM1 C7 C8 doub Y N 127 DM1 C7 C18 sing Y N 128 DM1 C8 O8 sing N N 129 DM1 C8 C9 sing Y N 130 DM1 O8 HO8 sing N N 131 DM1 C9 C10 sing N N 132 DM1 C9 C16 doub Y N 133 DM1 C10 O10 sing N N 134 DM1 C10 C11 sing N N 135 DM1 C10 H10 sing N N 136 DM1 O10 "C1'" sing N N 137 DM1 C11 C12 sing N N 138 DM1 C11 H111 sing N N 139 DM1 C11 H112 sing N N 140 DM1 C12 O12 sing N N 141 DM1 C12 C13 sing N N 142 DM1 C12 C15 sing N N 143 DM1 O12 HO12 sing N N 144 DM1 C13 O13 doub N N 145 DM1 C13 C14 sing N N 146 DM1 C14 H141 sing N N 147 DM1 C14 H142 sing N N 148 DM1 C14 H143 sing N N 149 DM1 C15 C16 sing N N 150 DM1 C15 H151 sing N N 151 DM1 C15 H152 sing N N 152 DM1 C16 C17 sing Y N 153 DM1 C17 O17 sing N N 154 DM1 C17 C18 doub Y N 155 DM1 O17 HO17 sing N N 156 DM1 C18 C19 sing N N 157 DM1 C19 O19 doub N N 158 DM1 C19 C20 sing N N 159 DM1 C21 H211 sing N N 160 DM1 C21 H212 sing N N 161 DM1 C21 H213 sing N N 162 DM1 "C1'" "C2'" sing N N 163 DM1 "C1'" "O5'" sing N N 164 DM1 "C1'" "H1'" sing N N 165 DM1 "C2'" "C3'" sing N N 166 DM1 "C2'" "H2'1" sing N N 167 DM1 "C2'" "H2'2" sing N N 168 DM1 "C3'" "N3'" sing N N 169 DM1 "C3'" "C4'" sing N N 170 DM1 "C3'" "H3'" sing N N 171 DM1 "N3'" "HN'1" sing N N 172 DM1 "N3'" "HN'2" sing N N 173 DM1 "C4'" "O4'" sing N N 174 DM1 "C4'" "C5'" sing N N 175 DM1 "C4'" "H4'" sing N N 176 DM1 "O4'" "HO4'" sing N N 177 DM1 "C5'" "O5'" sing N N 178 DM1 "C5'" "C6'" sing N N 179 DM1 "C5'" "H5'" sing N N 180 DM1 "C6'" "H6'1" sing N N 181 DM1 "C6'" "H6'2" sing N N 182 DM1 "C6'" "H6'3" sing N N 183 DT OP3 P sing N N 184 DT OP3 HOP3 sing N N 185 DT P OP1 doub N N 186 DT P OP2 sing N N 187 DT P "O5'" sing N N 188 DT OP2 HOP2 sing N N 189 DT "O5'" "C5'" sing N N 190 DT "C5'" "C4'" sing N N 191 DT "C5'" "H5'" sing N N 192 DT "C5'" "H5''" sing N N 193 DT "C4'" "O4'" sing N N 194 DT "C4'" "C3'" sing N N 195 DT "C4'" "H4'" sing N N 196 DT "O4'" "C1'" sing N N 197 DT "C3'" "O3'" sing N N 198 DT "C3'" "C2'" sing N N 199 DT "C3'" "H3'" sing N N 200 DT "O3'" "HO3'" sing N N 201 DT "C2'" "C1'" sing N N 202 DT "C2'" "H2'" sing N N 203 DT "C2'" "H2''" sing N N 204 DT "C1'" N1 sing N N 205 DT "C1'" "H1'" sing N N 206 DT N1 C2 sing N N 207 DT N1 C6 sing N N 208 DT C2 O2 doub N N 209 DT C2 N3 sing N N 210 DT N3 C4 sing N N 211 DT N3 H3 sing N N 212 DT C4 O4 doub N N 213 DT C4 C5 sing N N 214 DT C5 C7 sing N N 215 DT C5 C6 doub N N 216 DT C7 H71 sing N N 217 DT C7 H72 sing N N 218 DT C7 H73 sing N N 219 DT C6 H6 sing N N 220 HOH O H1 sing N N 221 HOH O H2 sing N N 222 # _ndb_struct_conf_na.entry_id 1VTH _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 A DA 6 8_665 0.179 -0.255 0.050 10.500 -1.174 0.364 1 A_DT1:DA6_A A 1 ? A 6 ? 20 1 1 A DG 2 1_555 A DC 5 8_665 -0.048 -0.313 -0.659 -19.808 5.486 -2.919 2 A_DG2:DC5_A A 2 ? A 5 ? 19 1 1 A DT 3 1_555 A DA 4 8_665 -0.313 -0.195 0.057 -4.833 -7.888 6.036 3 A_DT3:DA4_A A 3 ? A 4 ? 20 1 1 A DA 4 1_555 A DT 3 8_665 0.313 -0.195 0.057 4.833 -7.888 6.036 4 A_DA4:DT3_A A 4 ? A 3 ? 20 1 1 A DC 5 1_555 A DG 2 8_665 0.048 -0.313 -0.659 19.808 5.486 -2.919 5 A_DC5:DG2_A A 5 ? A 2 ? 19 1 1 A DA 6 1_555 A DT 1 8_665 -0.179 -0.255 0.050 -10.500 -1.174 0.364 6 A_DA6:DT1_A A 6 ? A 1 ? 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 A DA 6 8_665 A DG 2 1_555 A DC 5 8_665 0.886 1.434 7.179 3.524 -2.692 35.521 3.182 -0.330 7.107 -4.391 -5.749 35.788 1 AA_DT1DG2:DC5DA6_AA A 1 ? A 6 ? A 2 ? A 5 ? 1 A DG 2 1_555 A DC 5 8_665 A DT 3 1_555 A DA 4 8_665 -0.881 0.026 2.992 -5.261 -2.083 27.033 0.531 0.642 3.094 -4.396 11.100 27.608 2 AA_DG2DT3:DA4DC5_AA A 2 ? A 5 ? A 3 ? A 4 ? 1 A DT 3 1_555 A DA 4 8_665 A DA 4 1_555 A DT 3 8_665 0.000 -0.070 3.257 0.000 9.827 40.574 -1.128 0.000 3.157 13.925 0.000 41.698 3 AA_DT3DA4:DT3DA4_AA A 3 ? A 4 ? A 4 ? A 3 ? 1 A DA 4 1_555 A DT 3 8_665 A DC 5 1_555 A DG 2 8_665 0.881 0.026 2.992 5.261 -2.083 27.033 0.531 -0.642 3.094 -4.396 -11.101 27.608 4 AA_DA4DC5:DG2DT3_AA A 4 ? A 3 ? A 5 ? A 2 ? 1 A DC 5 1_555 A DG 2 8_665 A DA 6 1_555 A DT 1 8_665 -0.886 1.434 7.179 -3.524 -2.692 35.521 3.182 0.330 7.107 -4.391 5.749 35.788 5 AA_DC5DA6:DT1DG2_AA A 5 ? A 2 ? A 6 ? A 1 ? # _atom_sites.entry_id 1VTH _atom_sites.fract_transf_matrix[1][1] 0.035689 _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] 0.035689 _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] 0.018972 _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_ #