data_452D # _entry.id 452D # _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 452D pdb_0000452d 10.2210/pdb452d/pdb NDB DD0012 ? ? RCSB RCSB001344 ? ? WWPDB D_1000001344 ? ? # 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 2003-03-04 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 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' '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' pdbx_struct_special_symmetry 5 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 452D _pdbx_database_status.recvd_initial_deposition_date 1999-02-18 _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 'Thorpe, J.H.' 1 'Todd, A.K.' 2 'Cardin, C.J.' 3 # _citation.id primary _citation.title ;Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethlyamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray structure complexed to d(CG(5Br-U)ACG)2 at 1.3-angstrom resolution ; _citation.journal_abbrev J.Med.Chem. _citation.journal_volume 42 _citation.page_first 536 _citation.page_last 540 _citation.year 1999 _citation.journal_id_ASTM JMCMAR _citation.country US _citation.journal_id_ISSN 0022-2623 _citation.journal_id_CSD 0151 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10052960 _citation.pdbx_database_id_DOI 10.1021/jm980479u # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Todd, A.K.' 1 ? primary 'Adams, A.' 2 ? primary 'Thorpe, J.H.' 3 ? primary 'Denny, W.A.' 4 ? primary 'Wakelin, L.P.G.' 5 ? primary 'Cardin, C.J.' 6 ? # 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(*CP*GP*TP*AP*CP*G)-3') ; 1809.217 1 ? ? ? ? 2 non-polymer syn '9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4-CARBOXAMIDE' 308.378 2 ? ? ? ? 3 non-polymer syn '(4S)-2-METHYL-2,4-PENTANEDIOL' 118.174 1 ? ? ? ? 4 water nat water 18.015 29 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4-CARBOXAMIDE' 9AD 3 '(4S)-2-METHYL-2,4-PENTANEDIOL' MPD 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DT n 1 4 DA n 1 5 DC n 1 6 DG n # 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 9AD non-polymer . '9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4-CARBOXAMIDE' ? 'C18 H20 N4 O' 308.378 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 MPD non-polymer . '(4S)-2-METHYL-2,4-PENTANEDIOL' ? 'C6 H14 O2' 118.174 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1001 1001 DC C A . n A 1 2 DG 2 1002 1002 DG G A . n A 1 3 DT 3 1003 1003 DT T A . n A 1 4 DA 4 1004 1004 DA A A . n A 1 5 DC 5 1005 1005 DC C A . n A 1 6 DG 6 1006 1006 DG G 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 9AD 1 3013 3013 9AD 9AD A . C 2 9AD 1 3015 3015 9AD 9AD A . D 3 MPD 1 3016 3016 MPD MPD A . E 4 HOH 1 4001 4001 HOH HOH A . E 4 HOH 2 4002 4002 HOH HOH A . E 4 HOH 3 4003 4003 HOH HOH A . E 4 HOH 4 4004 4004 HOH HOH A . E 4 HOH 5 4005 4005 HOH HOH A . E 4 HOH 6 4006 4006 HOH HOH A . E 4 HOH 7 4007 4007 HOH HOH A . E 4 HOH 8 4008 4008 HOH HOH A . E 4 HOH 9 4009 4009 HOH HOH A . E 4 HOH 10 4010 4010 HOH HOH A . E 4 HOH 11 4011 4011 HOH HOH A . E 4 HOH 12 4012 4012 HOH HOH A . E 4 HOH 13 4013 4013 HOH HOH A . E 4 HOH 14 4014 4014 HOH HOH A . E 4 HOH 15 4015 4015 HOH HOH A . E 4 HOH 16 4016 4016 HOH HOH A . E 4 HOH 17 4017 4017 HOH HOH A . E 4 HOH 18 4018 4018 HOH HOH A . E 4 HOH 19 4019 4019 HOH HOH A . E 4 HOH 20 4020 4020 HOH HOH A . E 4 HOH 21 4021 4021 HOH HOH A . E 4 HOH 22 4022 4022 HOH HOH A . E 4 HOH 23 4023 4023 HOH HOH A . E 4 HOH 24 4024 4024 HOH HOH A . E 4 HOH 25 4025 4025 HOH HOH A . E 4 HOH 26 4026 4026 HOH HOH A . E 4 HOH 27 4027 4027 HOH HOH A . E 4 HOH 28 4028 4028 HOH HOH A . E 4 HOH 29 4029 4029 HOH HOH A . # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag N _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id MPD _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 3016 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id C5 _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id D _pdbx_unobs_or_zero_occ_atoms.label_comp_id MPD _pdbx_unobs_or_zero_occ_atoms.label_seq_id 1 _pdbx_unobs_or_zero_occ_atoms.label_atom_id C5 # _software.name SHELXL-97 _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 452D _cell.length_a 30.161 _cell.length_b 30.161 _cell.length_c 39.692 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 452D _symmetry.space_group_name_H-M 'P 64' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 172 # _exptl.entry_id 452D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 55.41 _exptl_crystal.density_Matthews 2.76 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type ? _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 452D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 16.0 _reflns.d_resolution_high 1.6 _reflns.number_obs ? _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 452D _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 16.0 _refine.ls_d_res_high 1.6 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.2017 _refine.ls_R_factor_all 0.2017 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.2556 _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 872 _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 ? _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.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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_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 188 _refine_hist.pdbx_number_atoms_ligand 87 _refine_hist.number_atoms_solvent 46 _refine_hist.number_atoms_total 321 _refine_hist.d_res_high 1.6 _refine_hist.d_res_low 16.0 # _database_PDB_matrix.entry_id 452D _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 452D _struct.title 'ACRIDINE BINDING TO DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 452D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'INTERCALATION, GROOVE BINDING, 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 2 ? D N N 3 ? E N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 452D _struct_ref.pdbx_db_accession 452D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 452D _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 452D _struct_ref_seq.db_align_beg 1001 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1006 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1001 _struct_ref_seq.pdbx_auth_seq_align_end 1006 # _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,D,E # 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' 4_655 -x+1,-y,z -1.0000000000 0.0000000000 0.0000000000 30.1610000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 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 1 N3 ? ? ? 1_555 A DG 6 N1 ? ? A DC 1001 A DG 1006 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 6 O6 ? ? A DC 1001 A DG 1006 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 6 N2 ? ? A DC 1001 A DG 1006 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 1002 A DC 1005 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 1002 A DC 1005 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 1002 A DC 1005 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 1003 A DA 1004 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 1003 A DA 1004 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 3 N3 ? ? A DA 1004 A DT 1003 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 3 O4 ? ? A DA 1004 A DT 1003 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 2 N1 ? ? A DC 1005 A DG 1002 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 2 O6 ? ? A DC 1005 A DG 1002 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 2 N2 ? ? A DC 1005 A DG 1002 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 1006 A DC 1001 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 1006 A DC 1001 4_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 1006 A DC 1001 4_655 ? ? ? ? ? ? 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 9AD 3013 ? 8 'BINDING SITE FOR RESIDUE 9AD A 3013' AC2 Software A 9AD 3015 ? 9 'BINDING SITE FOR RESIDUE 9AD A 3015' AC3 Software A MPD 3016 ? 5 'BINDING SITE FOR RESIDUE MPD A 3016' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 8 DC A 1 ? DC A 1001 . ? 4_655 ? 2 AC1 8 DG A 2 ? DG A 1002 . ? 4_655 ? 3 AC1 8 DG A 2 ? DG A 1002 . ? 6_544 ? 4 AC1 8 DA A 4 ? DA A 1004 . ? 1_555 ? 5 AC1 8 DC A 5 ? DC A 1005 . ? 1_555 ? 6 AC1 8 DG A 6 ? DG A 1006 . ? 1_555 ? 7 AC1 8 HOH E . ? HOH A 4012 . ? 5_555 ? 8 AC1 8 HOH E . ? HOH A 4027 . ? 6_544 ? 9 AC2 9 DC A 1 ? DC A 1001 . ? 1_445 ? 10 AC2 9 DC A 1 ? DC A 1001 . ? 4_655 ? 11 AC2 9 DC A 5 ? DC A 1005 . ? 5_555 ? 12 AC2 9 DG A 6 ? DG A 1006 . ? 4_545 ? 13 AC2 9 DG A 6 ? DG A 1006 . ? 1_555 ? 14 AC2 9 MPD D . ? MPD A 3016 . ? 4_545 ? 15 AC2 9 MPD D . ? MPD A 3016 . ? 1_555 ? 16 AC2 9 HOH E . ? HOH A 4002 . ? 2_545 ? 17 AC2 9 HOH E . ? HOH A 4023 . ? 1_555 ? 18 AC3 5 DG A 6 ? DG A 1006 . ? 1_555 ? 19 AC3 5 DG A 6 ? DG A 1006 . ? 4_545 ? 20 AC3 5 9AD C . ? 9AD A 3015 . ? 1_555 ? 21 AC3 5 9AD C . ? 9AD A 3015 . ? 4_545 ? 22 AC3 5 HOH E . ? HOH A 4008 . ? 4_545 ? # 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 "C1'" A DG 1002 ? ? N9 A DG 1002 ? ? 1.609 1.488 0.121 0.013 N 2 1 "C1'" A DG 1006 ? ? N9 A DG 1006 ? ? 1.598 1.488 0.110 0.013 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 DC 1001 ? ? "C5'" A DC 1001 ? ? "C4'" A DC 1001 ? ? 103.70 109.40 -5.70 0.80 N 2 1 "C5'" A DC 1001 ? ? "C4'" A DC 1001 ? ? "O4'" A DC 1001 ? ? 119.35 109.80 9.55 1.10 N 3 1 "O4'" A DG 1002 ? ? "C1'" A DG 1002 ? ? N9 A DG 1002 ? ? 99.42 108.00 -8.58 0.70 N 4 1 "C3'" A DT 1003 ? ? "C2'" A DT 1003 ? ? "C1'" A DT 1003 ? ? 97.09 102.40 -5.31 0.80 N 5 1 C2 A DT 1003 ? ? N3 A DT 1003 ? ? C4 A DT 1003 ? ? 132.42 127.20 5.22 0.60 N 6 1 C5 A DT 1003 ? ? C6 A DT 1003 ? ? N1 A DT 1003 ? ? 127.37 123.70 3.67 0.60 N 7 1 N3 A DT 1003 ? ? C2 A DT 1003 ? ? O2 A DT 1003 ? ? 127.07 122.30 4.77 0.60 N 8 1 C4 A DT 1003 ? ? C5 A DT 1003 ? ? C7 A DT 1003 ? ? 104.27 119.00 -14.73 0.60 N 9 1 C6 A DT 1003 ? ? C5 A DT 1003 ? ? C7 A DT 1003 ? ? 138.70 122.90 15.80 0.60 N 10 1 "O5'" A DA 1004 ? ? "C5'" A DA 1004 ? ? "C4'" A DA 1004 ? ? 103.79 109.40 -5.61 0.80 N 11 1 "O4'" A DA 1004 ? ? "C1'" A DA 1004 ? ? N9 A DA 1004 ? ? 101.58 108.00 -6.42 0.70 N 12 1 "O4'" A DC 1005 ? ? "C1'" A DC 1005 ? ? N1 A DC 1005 ? ? 113.10 108.30 4.80 0.30 N 13 1 "O5'" A DG 1006 ? ? "C5'" A DG 1006 ? ? "C4'" A DG 1006 ? ? 103.05 109.40 -6.35 0.80 N 14 1 "C3'" A DG 1006 ? ? "C2'" A DG 1006 ? ? "C1'" A DG 1006 ? ? 97.41 102.40 -4.99 0.80 N 15 1 "O4'" A DG 1006 ? ? "C1'" A DG 1006 ? ? N9 A DG 1006 ? ? 99.77 108.00 -8.23 0.70 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'INTERCALATION, GROOVE BINDER' # _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 MPD _pdbx_struct_special_symmetry.auth_seq_id 3016 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id MPD _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 9AD C1 C Y N 1 9AD C2 C Y N 2 9AD C3 C Y N 3 9AD C4 C Y N 4 9AD C5 C Y N 5 9AD C6 C Y N 6 9AD C7 C Y N 7 9AD C8 C Y N 8 9AD C9 C Y N 9 9AD N10 N Y N 10 9AD C11 C Y N 11 9AD C12 C Y N 12 9AD C13 C Y N 13 9AD C14 C Y N 14 9AD N9 N N N 15 9AD CD1 C N N 16 9AD OD1 O N N 17 9AD ND1 N N N 18 9AD ND2 N N N 19 9AD CD2 C N N 20 9AD CD3 C N N 21 9AD CD7 C N N 22 9AD CD8 C N N 23 9AD H1 H N N 24 9AD H2 H N N 25 9AD H3 H N N 26 9AD H5 H N N 27 9AD H6 H N N 28 9AD H7 H N N 29 9AD H8 H N N 30 9AD H9A H N N 31 9AD H9B H N N 32 9AD HD1 H N N 33 9AD HD21 H N N 34 9AD HD22 H N N 35 9AD HD31 H N N 36 9AD HD32 H N N 37 9AD HD71 H N N 38 9AD HD72 H N N 39 9AD HD73 H N N 40 9AD HD81 H N N 41 9AD HD82 H N N 42 9AD HD83 H N N 43 DA OP3 O N N 44 DA P P N N 45 DA OP1 O N N 46 DA OP2 O N N 47 DA "O5'" O N N 48 DA "C5'" C N N 49 DA "C4'" C N R 50 DA "O4'" O N N 51 DA "C3'" C N S 52 DA "O3'" O N N 53 DA "C2'" C N N 54 DA "C1'" C N R 55 DA N9 N Y N 56 DA C8 C Y N 57 DA N7 N Y N 58 DA C5 C Y N 59 DA C6 C Y N 60 DA N6 N N N 61 DA N1 N Y N 62 DA C2 C Y N 63 DA N3 N Y N 64 DA C4 C Y N 65 DA HOP3 H N N 66 DA HOP2 H N N 67 DA "H5'" H N N 68 DA "H5''" H N N 69 DA "H4'" H N N 70 DA "H3'" H N N 71 DA "HO3'" H N N 72 DA "H2'" H N N 73 DA "H2''" H N N 74 DA "H1'" H N N 75 DA H8 H N N 76 DA H61 H N N 77 DA H62 H N N 78 DA H2 H N N 79 DC OP3 O N N 80 DC P P N N 81 DC OP1 O N N 82 DC OP2 O N N 83 DC "O5'" O N N 84 DC "C5'" C N N 85 DC "C4'" C N R 86 DC "O4'" O N N 87 DC "C3'" C N S 88 DC "O3'" O N N 89 DC "C2'" C N N 90 DC "C1'" C N R 91 DC N1 N N N 92 DC C2 C N N 93 DC O2 O N N 94 DC N3 N N N 95 DC C4 C N N 96 DC N4 N N N 97 DC C5 C N N 98 DC C6 C N N 99 DC HOP3 H N N 100 DC HOP2 H N N 101 DC "H5'" H N N 102 DC "H5''" H N N 103 DC "H4'" H N N 104 DC "H3'" H N N 105 DC "HO3'" H N N 106 DC "H2'" H N N 107 DC "H2''" H N N 108 DC "H1'" H N N 109 DC H41 H N N 110 DC H42 H N N 111 DC H5 H N N 112 DC H6 H N N 113 DG OP3 O N N 114 DG P P N N 115 DG OP1 O N N 116 DG OP2 O N N 117 DG "O5'" O N N 118 DG "C5'" C N N 119 DG "C4'" C N R 120 DG "O4'" O N N 121 DG "C3'" C N S 122 DG "O3'" O N N 123 DG "C2'" C N N 124 DG "C1'" C N R 125 DG N9 N Y N 126 DG C8 C Y N 127 DG N7 N Y N 128 DG C5 C Y N 129 DG C6 C N N 130 DG O6 O N N 131 DG N1 N N N 132 DG C2 C N N 133 DG N2 N N N 134 DG N3 N N N 135 DG C4 C Y N 136 DG HOP3 H N N 137 DG HOP2 H N N 138 DG "H5'" H N N 139 DG "H5''" H N N 140 DG "H4'" H N N 141 DG "H3'" H N N 142 DG "HO3'" H N N 143 DG "H2'" H N N 144 DG "H2''" H N N 145 DG "H1'" H N N 146 DG H8 H N N 147 DG H1 H N N 148 DG H21 H N N 149 DG H22 H N N 150 DT OP3 O N N 151 DT P P N N 152 DT OP1 O N N 153 DT OP2 O N N 154 DT "O5'" O N N 155 DT "C5'" C N N 156 DT "C4'" C N R 157 DT "O4'" O N N 158 DT "C3'" C N S 159 DT "O3'" O N N 160 DT "C2'" C N N 161 DT "C1'" C N R 162 DT N1 N N N 163 DT C2 C N N 164 DT O2 O N N 165 DT N3 N N N 166 DT C4 C N N 167 DT O4 O N N 168 DT C5 C N N 169 DT C7 C N N 170 DT C6 C N N 171 DT HOP3 H N N 172 DT HOP2 H N N 173 DT "H5'" H N N 174 DT "H5''" H N N 175 DT "H4'" H N N 176 DT "H3'" H N N 177 DT "HO3'" H N N 178 DT "H2'" H N N 179 DT "H2''" H N N 180 DT "H1'" H N N 181 DT H3 H N N 182 DT H71 H N N 183 DT H72 H N N 184 DT H73 H N N 185 DT H6 H N N 186 HOH O O N N 187 HOH H1 H N N 188 HOH H2 H N N 189 MPD C1 C N N 190 MPD C2 C N N 191 MPD O2 O N N 192 MPD CM C N N 193 MPD C3 C N N 194 MPD C4 C N S 195 MPD O4 O N N 196 MPD C5 C N N 197 MPD H11 H N N 198 MPD H12 H N N 199 MPD H13 H N N 200 MPD HO2 H N N 201 MPD HM1 H N N 202 MPD HM2 H N N 203 MPD HM3 H N N 204 MPD H31 H N N 205 MPD H32 H N N 206 MPD H4 H N N 207 MPD HO4 H N N 208 MPD H51 H N N 209 MPD H52 H N N 210 MPD H53 H N N 211 # 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 9AD C1 C2 doub Y N 1 9AD C1 C11 sing Y N 2 9AD C1 H1 sing N N 3 9AD C2 C3 sing Y N 4 9AD C2 H2 sing N N 5 9AD C3 C4 doub Y N 6 9AD C3 H3 sing N N 7 9AD C4 C12 sing Y N 8 9AD C4 CD1 sing N N 9 9AD C5 C6 doub Y N 10 9AD C5 C14 sing Y N 11 9AD C5 H5 sing N N 12 9AD C6 C7 sing Y N 13 9AD C6 H6 sing N N 14 9AD C7 C8 doub Y N 15 9AD C7 H7 sing N N 16 9AD C8 C13 sing Y N 17 9AD C8 H8 sing N N 18 9AD C9 C11 doub Y N 19 9AD C9 C13 sing Y N 20 9AD C9 N9 sing N N 21 9AD N10 C12 doub Y N 22 9AD N10 C14 sing Y N 23 9AD C11 C12 sing Y N 24 9AD C13 C14 doub Y N 25 9AD N9 H9A sing N N 26 9AD N9 H9B sing N N 27 9AD CD1 OD1 doub N N 28 9AD CD1 ND1 sing N N 29 9AD ND1 CD2 sing N N 30 9AD ND1 HD1 sing N N 31 9AD ND2 CD3 sing N N 32 9AD ND2 CD7 sing N N 33 9AD ND2 CD8 sing N N 34 9AD CD2 CD3 sing N N 35 9AD CD2 HD21 sing N N 36 9AD CD2 HD22 sing N N 37 9AD CD3 HD31 sing N N 38 9AD CD3 HD32 sing N N 39 9AD CD7 HD71 sing N N 40 9AD CD7 HD72 sing N N 41 9AD CD7 HD73 sing N N 42 9AD CD8 HD81 sing N N 43 9AD CD8 HD82 sing N N 44 9AD CD8 HD83 sing N N 45 DA OP3 P sing N N 46 DA OP3 HOP3 sing N N 47 DA P OP1 doub N N 48 DA P OP2 sing N N 49 DA P "O5'" sing N N 50 DA OP2 HOP2 sing N N 51 DA "O5'" "C5'" sing N N 52 DA "C5'" "C4'" sing N N 53 DA "C5'" "H5'" sing N N 54 DA "C5'" "H5''" sing N N 55 DA "C4'" "O4'" sing N N 56 DA "C4'" "C3'" sing N N 57 DA "C4'" "H4'" sing N N 58 DA "O4'" "C1'" sing N N 59 DA "C3'" "O3'" sing N N 60 DA "C3'" "C2'" sing N N 61 DA "C3'" "H3'" sing N N 62 DA "O3'" "HO3'" sing N N 63 DA "C2'" "C1'" sing N N 64 DA "C2'" "H2'" sing N N 65 DA "C2'" "H2''" sing N N 66 DA "C1'" N9 sing N N 67 DA "C1'" "H1'" sing N N 68 DA N9 C8 sing Y N 69 DA N9 C4 sing Y N 70 DA C8 N7 doub Y N 71 DA C8 H8 sing N N 72 DA N7 C5 sing Y N 73 DA C5 C6 sing Y N 74 DA C5 C4 doub Y N 75 DA C6 N6 sing N N 76 DA C6 N1 doub Y N 77 DA N6 H61 sing N N 78 DA N6 H62 sing N N 79 DA N1 C2 sing Y N 80 DA C2 N3 doub Y N 81 DA C2 H2 sing N N 82 DA N3 C4 sing Y N 83 DC OP3 P sing N N 84 DC OP3 HOP3 sing N N 85 DC P OP1 doub N N 86 DC P OP2 sing N N 87 DC P "O5'" sing N N 88 DC OP2 HOP2 sing N N 89 DC "O5'" "C5'" sing N N 90 DC "C5'" "C4'" sing N N 91 DC "C5'" "H5'" sing N N 92 DC "C5'" "H5''" sing N N 93 DC "C4'" "O4'" sing N N 94 DC "C4'" "C3'" sing N N 95 DC "C4'" "H4'" sing N N 96 DC "O4'" "C1'" sing N N 97 DC "C3'" "O3'" sing N N 98 DC "C3'" "C2'" sing N N 99 DC "C3'" "H3'" sing N N 100 DC "O3'" "HO3'" sing N N 101 DC "C2'" "C1'" sing N N 102 DC "C2'" "H2'" sing N N 103 DC "C2'" "H2''" sing N N 104 DC "C1'" N1 sing N N 105 DC "C1'" "H1'" sing N N 106 DC N1 C2 sing N N 107 DC N1 C6 sing N N 108 DC C2 O2 doub N N 109 DC C2 N3 sing N N 110 DC N3 C4 doub N N 111 DC C4 N4 sing N N 112 DC C4 C5 sing N N 113 DC N4 H41 sing N N 114 DC N4 H42 sing N N 115 DC C5 C6 doub N N 116 DC C5 H5 sing N N 117 DC C6 H6 sing N N 118 DG OP3 P sing N N 119 DG OP3 HOP3 sing N N 120 DG P OP1 doub N N 121 DG P OP2 sing N N 122 DG P "O5'" sing N N 123 DG OP2 HOP2 sing N N 124 DG "O5'" "C5'" sing N N 125 DG "C5'" "C4'" sing N N 126 DG "C5'" "H5'" sing N N 127 DG "C5'" "H5''" sing N N 128 DG "C4'" "O4'" sing N N 129 DG "C4'" "C3'" sing N N 130 DG "C4'" "H4'" sing N N 131 DG "O4'" "C1'" sing N N 132 DG "C3'" "O3'" sing N N 133 DG "C3'" "C2'" sing N N 134 DG "C3'" "H3'" sing N N 135 DG "O3'" "HO3'" sing N N 136 DG "C2'" "C1'" sing N N 137 DG "C2'" "H2'" sing N N 138 DG "C2'" "H2''" sing N N 139 DG "C1'" N9 sing N N 140 DG "C1'" "H1'" sing N N 141 DG N9 C8 sing Y N 142 DG N9 C4 sing Y N 143 DG C8 N7 doub Y N 144 DG C8 H8 sing N N 145 DG N7 C5 sing Y N 146 DG C5 C6 sing N N 147 DG C5 C4 doub Y N 148 DG C6 O6 doub N N 149 DG C6 N1 sing N N 150 DG N1 C2 sing N N 151 DG N1 H1 sing N N 152 DG C2 N2 sing N N 153 DG C2 N3 doub N N 154 DG N2 H21 sing N N 155 DG N2 H22 sing N N 156 DG N3 C4 sing N N 157 DT OP3 P sing N N 158 DT OP3 HOP3 sing N N 159 DT P OP1 doub N N 160 DT P OP2 sing N N 161 DT P "O5'" sing N N 162 DT OP2 HOP2 sing N N 163 DT "O5'" "C5'" sing N N 164 DT "C5'" "C4'" sing N N 165 DT "C5'" "H5'" sing N N 166 DT "C5'" "H5''" sing N N 167 DT "C4'" "O4'" sing N N 168 DT "C4'" "C3'" sing N N 169 DT "C4'" "H4'" sing N N 170 DT "O4'" "C1'" sing N N 171 DT "C3'" "O3'" sing N N 172 DT "C3'" "C2'" sing N N 173 DT "C3'" "H3'" sing N N 174 DT "O3'" "HO3'" sing N N 175 DT "C2'" "C1'" sing N N 176 DT "C2'" "H2'" sing N N 177 DT "C2'" "H2''" sing N N 178 DT "C1'" N1 sing N N 179 DT "C1'" "H1'" sing N N 180 DT N1 C2 sing N N 181 DT N1 C6 sing N N 182 DT C2 O2 doub N N 183 DT C2 N3 sing N N 184 DT N3 C4 sing N N 185 DT N3 H3 sing N N 186 DT C4 O4 doub N N 187 DT C4 C5 sing N N 188 DT C5 C7 sing N N 189 DT C5 C6 doub N N 190 DT C7 H71 sing N N 191 DT C7 H72 sing N N 192 DT C7 H73 sing N N 193 DT C6 H6 sing N N 194 HOH O H1 sing N N 195 HOH O H2 sing N N 196 MPD C1 C2 sing N N 197 MPD C1 H11 sing N N 198 MPD C1 H12 sing N N 199 MPD C1 H13 sing N N 200 MPD C2 O2 sing N N 201 MPD C2 CM sing N N 202 MPD C2 C3 sing N N 203 MPD O2 HO2 sing N N 204 MPD CM HM1 sing N N 205 MPD CM HM2 sing N N 206 MPD CM HM3 sing N N 207 MPD C3 C4 sing N N 208 MPD C3 H31 sing N N 209 MPD C3 H32 sing N N 210 MPD C4 O4 sing N N 211 MPD C4 C5 sing N N 212 MPD C4 H4 sing N N 213 MPD O4 HO4 sing N N 214 MPD C5 H51 sing N N 215 MPD C5 H52 sing N N 216 MPD C5 H53 sing N N 217 # _ndb_struct_conf_na.entry_id 452D _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 1 1_555 A DG 6 4_655 0.031 -0.227 0.226 2.539 -13.763 -3.831 1 A_DC1001:DG1006_A A 1001 ? A 1006 ? 19 1 1 A DG 2 1_555 A DC 5 4_655 -0.274 -0.090 0.213 -4.551 -2.872 -1.761 2 A_DG1002:DC1005_A A 1002 ? A 1005 ? 19 1 1 A DT 3 1_555 A DA 4 4_655 0.062 -0.158 -0.005 3.183 -12.344 -0.579 3 A_DT1003:DA1004_A A 1003 ? A 1004 ? 20 1 1 A DA 4 1_555 A DT 3 4_655 -0.062 -0.158 -0.005 -3.183 -12.344 -0.579 4 A_DA1004:DT1003_A A 1004 ? A 1003 ? 20 1 1 A DC 5 1_555 A DG 2 4_655 0.274 -0.090 0.213 4.551 -2.872 -1.761 5 A_DC1005:DG1002_A A 1005 ? A 1002 ? 19 1 1 A DG 6 1_555 A DC 1 4_655 -0.031 -0.227 0.226 -2.539 -13.763 -3.831 6 A_DG1006:DC1001_A A 1006 ? A 1001 ? 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 1 1_555 A DG 6 4_655 A DG 2 1_555 A DC 5 4_655 0.344 0.291 6.835 -0.639 1.784 24.941 -0.437 -1.190 6.828 4.124 1.476 25.012 1 AA_DC1001DG1002:DC1005DG1006_AA A 1001 ? A 1006 ? A 1002 ? A 1005 ? 1 A DG 2 1_555 A DC 5 4_655 A DT 3 1_555 A DA 4 4_655 -0.536 0.007 3.217 1.966 2.135 28.688 -0.452 1.505 3.166 4.296 -3.954 28.832 2 AA_DG1002DT1003:DA1004DC1005_AA A 1002 ? A 1005 ? A 1003 ? A 1004 ? 1 A DT 3 1_555 A DA 4 4_655 A DA 4 1_555 A DT 3 4_655 0.000 1.677 3.281 0.000 -2.671 47.148 2.310 0.000 3.187 -3.336 0.000 47.219 3 AA_DT1003DA1004:DT1003DA1004_AA A 1003 ? A 1004 ? A 1004 ? A 1003 ? 1 A DA 4 1_555 A DT 3 4_655 A DC 5 1_555 A DG 2 4_655 0.536 0.007 3.217 -1.966 2.135 28.688 -0.452 -1.505 3.166 4.296 3.954 28.832 4 AA_DA1004DC1005:DG1002DT1003_AA A 1004 ? A 1003 ? A 1005 ? A 1002 ? 1 A DC 5 1_555 A DG 2 4_655 A DG 6 1_555 A DC 1 4_655 -0.344 0.291 6.835 0.639 1.784 24.941 -0.437 1.190 6.828 4.124 -1.476 25.012 5 AA_DC1005DG1006:DC1001DG1002_AA A 1005 ? A 1002 ? A 1006 ? A 1001 ? # _atom_sites.entry_id 452D _atom_sites.fract_transf_matrix[1][1] 0.033155 _atom_sites.fract_transf_matrix[1][2] 0.019142 _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] 0.038285 _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] 0.025194 _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 H N O P # loop_