data_408D # _entry.id 408D # _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 408D pdb_0000408d 10.2210/pdb408d/pdb RCSB BDD003 ? ? WWPDB D_1000179208 ? ? # 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 1998-10-19 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-28 # _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 408D _pdbx_database_status.recvd_initial_deposition_date 1998-06-24 _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 'Kielkopf, C.L.' 1 'White, S.' 2 'Szewczyk, J.W.' 3 'Turner, J.M.' 4 'Baird, E.E.' 5 'Dervan, P.B.' 6 'Rees, D.C.' 7 # _citation.id primary _citation.title 'A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA.' _citation.journal_abbrev Science _citation.journal_volume 282 _citation.page_first 111 _citation.page_last 115 _citation.year 1998 _citation.journal_id_ASTM SCIEAS _citation.country US _citation.journal_id_ISSN 0036-8075 _citation.journal_id_CSD 0038 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9756473 _citation.pdbx_database_id_DOI 10.1126/science.282.5386.111 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kielkopf, C.L.' 1 ? primary 'White, S.' 2 ? primary 'Szewczyk, J.W.' 3 ? primary 'Turner, J.M.' 4 ? primary 'Baird, E.E.' 5 ? primary 'Dervan, P.B.' 6 ? primary 'Rees, D.C.' 7 ? # 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 man ;DNA (5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3') ; 3045.004 2 ? ? ? ? 2 non-polymer syn 'IMIDAZOLE-PYRROLE POLYAMIDE' 648.736 2 ? ? ? ? 3 water nat water 18.015 87 ? ? ? ? # _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)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAGTACTGG _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 'IMIDAZOLE-PYRROLE POLYAMIDE' IPY 3 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 DC n 1 3 DA n 1 4 DG n 1 5 DT n 1 6 DA n 1 7 DC n 1 8 DT n 1 9 DG n 1 10 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 IPY non-polymer . 'IMIDAZOLE-PYRROLE POLYAMIDE' 'IMIDAZOLE-PYRROLE-PYRROLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE' 'C31 H42 N11 O5 1' 648.736 # 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 1 1 DC C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DC 1 11 11 DC C B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DA 3 13 13 DA A B . n B 1 4 DG 4 14 14 DG G B . n B 1 5 DT 5 15 15 DT T B . n B 1 6 DA 6 16 16 DA A B . n B 1 7 DC 7 17 17 DC C B . n B 1 8 DT 8 18 18 DT T B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DG 10 20 20 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 IPY 1 22 22 IPY IPY A . D 2 IPY 1 21 21 IPY IPY B . E 3 HOH 1 23 23 HOH HOH A . E 3 HOH 2 29 29 HOH HOH A . E 3 HOH 3 31 31 HOH HOH A . E 3 HOH 4 32 32 HOH HOH A . E 3 HOH 5 34 34 HOH HOH A . E 3 HOH 6 35 35 HOH HOH A . E 3 HOH 7 36 36 HOH HOH A . E 3 HOH 8 44 44 HOH HOH A . E 3 HOH 9 45 45 HOH HOH A . E 3 HOH 10 48 48 HOH HOH A . E 3 HOH 11 49 49 HOH HOH A . E 3 HOH 12 50 50 HOH HOH A . E 3 HOH 13 54 54 HOH HOH A . E 3 HOH 14 56 56 HOH HOH A . E 3 HOH 15 58 58 HOH HOH A . E 3 HOH 16 61 61 HOH HOH A . E 3 HOH 17 62 62 HOH HOH A . E 3 HOH 18 63 63 HOH HOH A . E 3 HOH 19 69 69 HOH HOH A . E 3 HOH 20 70 70 HOH HOH A . E 3 HOH 21 74 74 HOH HOH A . E 3 HOH 22 78 78 HOH HOH A . E 3 HOH 23 79 79 HOH HOH A . E 3 HOH 24 83 83 HOH HOH A . E 3 HOH 25 92 92 HOH HOH A . E 3 HOH 26 97 97 HOH HOH A . E 3 HOH 27 102 102 HOH HOH A . E 3 HOH 28 107 107 HOH HOH A . E 3 HOH 29 109 109 HOH HOH A . E 3 HOH 30 110 110 HOH HOH A . E 3 HOH 31 112 112 HOH HOH A . E 3 HOH 32 204 204 HOH HOH A . E 3 HOH 33 205 205 HOH HOH A . E 3 HOH 34 300 300 HOH HOH A . E 3 HOH 35 302 302 HOH HOH A . E 3 HOH 36 305 305 HOH HOH A . F 3 HOH 1 24 24 HOH HOH B . F 3 HOH 2 25 25 HOH HOH B . F 3 HOH 3 26 26 HOH HOH B . F 3 HOH 4 27 27 HOH HOH B . F 3 HOH 5 28 28 HOH HOH B . F 3 HOH 6 30 30 HOH HOH B . F 3 HOH 7 37 37 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 42 42 HOH HOH B . F 3 HOH 13 43 43 HOH HOH B . F 3 HOH 14 46 46 HOH HOH B . F 3 HOH 15 47 47 HOH HOH B . F 3 HOH 16 51 51 HOH HOH B . F 3 HOH 17 52 52 HOH HOH B . F 3 HOH 18 55 55 HOH HOH B . F 3 HOH 19 57 57 HOH HOH B . F 3 HOH 20 59 59 HOH HOH B . F 3 HOH 21 64 64 HOH HOH B . F 3 HOH 22 65 65 HOH HOH B . F 3 HOH 23 67 67 HOH HOH B . F 3 HOH 24 68 68 HOH HOH B . F 3 HOH 25 71 71 HOH HOH B . F 3 HOH 26 73 73 HOH HOH B . F 3 HOH 27 76 76 HOH HOH B . F 3 HOH 28 80 80 HOH HOH B . F 3 HOH 29 81 81 HOH HOH B . F 3 HOH 30 88 88 HOH HOH B . F 3 HOH 31 94 94 HOH HOH B . F 3 HOH 32 95 95 HOH HOH B . F 3 HOH 33 96 96 HOH HOH B . F 3 HOH 34 98 98 HOH HOH B . F 3 HOH 35 99 99 HOH HOH B . F 3 HOH 36 101 101 HOH HOH B . F 3 HOH 37 103 103 HOH HOH B . F 3 HOH 38 104 104 HOH HOH B . F 3 HOH 39 108 108 HOH HOH B . F 3 HOH 40 111 111 HOH HOH B . F 3 HOH 41 115 115 HOH HOH B . F 3 HOH 42 202 202 HOH HOH B . F 3 HOH 43 203 203 HOH HOH B . F 3 HOH 44 208 208 HOH HOH B . F 3 HOH 45 212 212 HOH HOH B . F 3 HOH 46 213 213 HOH HOH B . F 3 HOH 47 301 301 HOH HOH B . F 3 HOH 48 303 303 HOH HOH B . F 3 HOH 49 304 304 HOH HOH B . F 3 HOH 50 306 306 HOH HOH B . F 3 HOH 51 307 307 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR refinement 3.1 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 # _cell.entry_id 408D _cell.length_a 60.660 _cell.length_b 30.200 _cell.length_c 43.460 _cell.angle_alpha 90.00 _cell.angle_beta 123.59 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 408D _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting monoclinic _symmetry.Int_Tables_number 5 # _exptl.entry_id 408D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.72 _exptl_crystal.density_percent_sol 54.82 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.50 _exptl_crystal_grow.pdbx_details 'pH 7.50, VAPOR DIFFUSION, HANGING DROP, 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 'CALCIUM ACETATE' ? ? ? 1 2 1 MPD ? ? ? 1 3 1 TRIS ? ? ? 1 4 2 'CALCIUM ACETATE' ? ? ? 1 5 2 MPD ? ? ? 1 6 2 TRIS ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 103.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type RIGAKU _diffrn_detector.pdbx_collection_date 1997-11-15 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _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 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 408D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F 0.000 _reflns.d_resolution_low 16.000 _reflns.d_resolution_high 2.100 _reflns.number_obs 3417 _reflns.number_all 3417 _reflns.percent_possible_obs 91.000 _reflns.pdbx_Rmerge_I_obs 0.0380000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.600 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 408D _refine.ls_number_reflns_obs 3402 _refine.ls_number_reflns_all 3583 _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 20.000 _refine.ls_d_res_high 2.100 _refine.ls_percent_reflns_obs 91.000 _refine.ls_R_factor_obs 0.2190000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2190000 _refine.ls_R_factor_R_free 0.2420000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.600 _refine.ls_number_reflns_R_free 181 _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.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_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 404 _refine_hist.pdbx_number_atoms_ligand 104 _refine_hist.number_atoms_solvent 87 _refine_hist.number_atoms_total 595 _refine_hist.d_res_high 2.100 _refine_hist.d_res_low 20.000 # 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 x_bond_d 0.012 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 1.29 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_xplor_file.serial_no 1 _pdbx_xplor_file.param_file NOC2ENDO.PARAM _pdbx_xplor_file.topol_file IPPP_NODIH.PAR _pdbx_xplor_file.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 408D _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 408D _struct.title 'STRUCTURAL BASIS FOR RECOGNITION OF A-T AND T-A BASE PAIRS IN THE MINOR GROOVE OF B-DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 408D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DRUG IN THE DNA MINOR GROOVE, 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 408D _struct_ref.pdbx_db_accession 408D _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 408D A 1 ? 10 ? 408D 1 ? 10 ? 1 10 2 1 408D B 1 ? 10 ? 408D 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,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 DC 1 O2 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog2 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog3 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 8 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 8 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? # _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 IPY 21 ? 17 'BINDING SITE FOR RESIDUE IPY B 21' AC2 Software A IPY 22 ? 17 'BINDING SITE FOR RESIDUE IPY A 22' 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 17 DA A 3 ? DA A 3 . ? 1_555 ? 2 AC1 17 DG A 4 ? DG A 4 . ? 1_555 ? 3 AC1 17 IPY C . ? IPY A 22 . ? 1_555 ? 4 AC1 17 DC B 1 ? DC B 11 . ? 2_656 ? 5 AC1 17 DG B 4 ? DG B 14 . ? 1_555 ? 6 AC1 17 DT B 5 ? DT B 15 . ? 1_555 ? 7 AC1 17 DA B 6 ? DA B 16 . ? 1_555 ? 8 AC1 17 DC B 7 ? DC B 17 . ? 1_555 ? 9 AC1 17 DT B 8 ? DT B 18 . ? 1_555 ? 10 AC1 17 DG B 9 ? DG B 19 . ? 1_555 ? 11 AC1 17 DG B 10 ? DG B 20 . ? 1_555 ? 12 AC1 17 DG B 10 ? DG B 20 . ? 4_546 ? 13 AC1 17 HOH F . ? HOH B 51 . ? 4_546 ? 14 AC1 17 HOH F . ? HOH B 94 . ? 1_555 ? 15 AC1 17 HOH F . ? HOH B 213 . ? 1_555 ? 16 AC1 17 HOH F . ? HOH B 304 . ? 1_555 ? 17 AC1 17 HOH F . ? HOH B 307 . ? 1_555 ? 18 AC2 17 DC A 1 ? DC A 1 . ? 3_545 ? 19 AC2 17 DG A 4 ? DG A 4 . ? 1_555 ? 20 AC2 17 DT A 5 ? DT A 5 . ? 1_555 ? 21 AC2 17 DA A 6 ? DA A 6 . ? 1_555 ? 22 AC2 17 DC A 7 ? DC A 7 . ? 1_555 ? 23 AC2 17 DT A 8 ? DT A 8 . ? 1_555 ? 24 AC2 17 DG A 9 ? DG A 9 . ? 1_555 ? 25 AC2 17 DG A 10 ? DG A 10 . ? 1_555 ? 26 AC2 17 HOH E . ? HOH A 97 . ? 4_545 ? 27 AC2 17 DC B 1 ? DC B 11 . ? 2_656 ? 28 AC2 17 DC B 2 ? DC B 12 . ? 1_555 ? 29 AC2 17 DA B 3 ? DA B 13 . ? 1_555 ? 30 AC2 17 DG B 4 ? DG B 14 . ? 1_555 ? 31 AC2 17 DG B 10 ? DG B 20 . ? 4_546 ? 32 AC2 17 IPY D . ? IPY B 21 . ? 1_555 ? 33 AC2 17 HOH F . ? HOH B 40 . ? 4_546 ? 34 AC2 17 HOH F . ? HOH B 203 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "O5'" B DG 19 ? ? O B HOH 73 ? ? 2.03 2 1 O B HOH 37 ? ? O B HOH 115 ? ? 2.07 3 1 OP2 B DG 19 ? ? O B HOH 73 ? ? 2.09 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 109 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 39 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 3_545 _pdbx_validate_symm_contact.dist 1.94 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C6 _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DG _pdbx_validate_rmsd_bond.auth_seq_id_1 19 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 O6 _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DG _pdbx_validate_rmsd_bond.auth_seq_id_2 19 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.302 _pdbx_validate_rmsd_bond.bond_target_value 1.237 _pdbx_validate_rmsd_bond.bond_deviation 0.065 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.009 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DG A 4 ? ? 0.065 'SIDE CHAIN' 2 1 DT B 15 ? ? 0.077 'SIDE CHAIN' # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 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 IPY C C Y N 147 IPY C1 C Y N 148 IPY C2 C Y N 149 IPY C3 C N N 150 IPY C4 C Y N 151 IPY C5 C N N 152 IPY C6 C Y N 153 IPY C8 C Y N 154 IPY C9 C N N 155 IPY C10 C Y N 156 IPY C11 C N N 157 IPY C12 C Y N 158 IPY C13 C Y N 159 IPY C14 C Y N 160 IPY C15 C N N 161 IPY C16 C Y N 162 IPY C18 C N N 163 IPY C19 C N N 164 IPY C20 C N N 165 IPY C21 C N N 166 IPY C22 C N N 167 IPY C23 C N N 168 IPY C24 C N N 169 IPY C25 C Y N 170 IPY C26 C Y N 171 IPY C27 C Y N 172 IPY C28 C N N 173 IPY C29 C N N 174 IPY C30 C N N 175 IPY C31 C N N 176 IPY C32 C Y N 177 IPY O1 O N N 178 IPY O2 O N N 179 IPY O3 O N N 180 IPY O4 O N N 181 IPY O5 O N N 182 IPY N N Y N 183 IPY N1 N N N 184 IPY N3 N Y N 185 IPY N4 N N N 186 IPY N5 N Y N 187 IPY N6 N N N 188 IPY N7 N N N 189 IPY N8 N N N 190 IPY N9 N Y N 191 IPY N10 N Y N 192 IPY N11 N N N 193 IPY H1 H N N 194 IPY H2 H N N 195 IPY H31 H N N 196 IPY H32A H N N 197 IPY H33 H N N 198 IPY H8 H N N 199 IPY H91 H N N 200 IPY H92 H N N 201 IPY H93 H N N 202 IPY H13 H N N 203 IPY H14 H N N 204 IPY H151 H N N 205 IPY H152 H N N 206 IPY H153 H N N 207 IPY H181 H N N 208 IPY H182 H N N 209 IPY H191 H N N 210 IPY H192 H N N 211 IPY H201 H N N 212 IPY H202 H N N 213 IPY H211 H N N 214 IPY H212 H N N 215 IPY H213 H N N 216 IPY H221 H N N 217 IPY H222 H N N 218 IPY H223 H N N 219 IPY H26 H N N 220 IPY H27 H N N 221 IPY H281 H N N 222 IPY H282 H N N 223 IPY H283 H N N 224 IPY H291 H N N 225 IPY H292 H N N 226 IPY H301 H N N 227 IPY H302 H N N 228 IPY H32 H N N 229 IPY HN1 H N N 230 IPY HN4 H N N 231 IPY HN6 H N N 232 IPY HN7 H N N 233 IPY HN8 H N N 234 IPY H11 H N N 235 # 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 IPY C C2 doub Y N 152 IPY C C32 sing Y N 153 IPY C N8 sing N N 154 IPY C1 C6 sing Y N 155 IPY C1 C10 doub Y N 156 IPY C1 H1 sing N N 157 IPY C2 N sing Y N 158 IPY C2 H2 sing N N 159 IPY C3 N sing N N 160 IPY C3 H31 sing N N 161 IPY C3 H32A sing N N 162 IPY C3 H33 sing N N 163 IPY C4 C5 sing N N 164 IPY C4 C32 doub Y N 165 IPY C4 N sing Y N 166 IPY C5 O1 doub N N 167 IPY C5 N1 sing N N 168 IPY C6 C8 doub Y N 169 IPY C6 N1 sing N N 170 IPY C8 N3 sing Y N 171 IPY C8 H8 sing N N 172 IPY C9 N3 sing N N 173 IPY C9 H91 sing N N 174 IPY C9 H92 sing N N 175 IPY C9 H93 sing N N 176 IPY C10 C11 sing N N 177 IPY C10 N3 sing Y N 178 IPY C11 O2 doub N N 179 IPY C11 N4 sing N N 180 IPY C12 C13 sing Y N 181 IPY C12 C14 doub Y N 182 IPY C12 N4 sing N N 183 IPY C13 C16 doub Y N 184 IPY C13 H13 sing N N 185 IPY C14 N5 sing Y N 186 IPY C14 H14 sing N N 187 IPY C15 N5 sing N N 188 IPY C15 H151 sing N N 189 IPY C15 H152 sing N N 190 IPY C15 H153 sing N N 191 IPY C16 C23 sing N N 192 IPY C16 N5 sing Y N 193 IPY C18 C19 sing N N 194 IPY C18 N6 sing N N 195 IPY C18 H181 sing N N 196 IPY C18 H182 sing N N 197 IPY C19 C20 sing N N 198 IPY C19 H191 sing N N 199 IPY C19 H192 sing N N 200 IPY C20 N7 sing N N 201 IPY C20 H201 sing N N 202 IPY C20 H202 sing N N 203 IPY C21 N7 sing N N 204 IPY C21 H211 sing N N 205 IPY C21 H212 sing N N 206 IPY C21 H213 sing N N 207 IPY C22 N7 sing N N 208 IPY C22 H221 sing N N 209 IPY C22 H222 sing N N 210 IPY C22 H223 sing N N 211 IPY C23 O3 doub N N 212 IPY C23 N11 sing N N 213 IPY C24 C25 sing N N 214 IPY C24 O4 doub N N 215 IPY C24 N8 sing N N 216 IPY C25 N9 sing Y N 217 IPY C25 N10 doub Y N 218 IPY C26 C27 doub Y N 219 IPY C26 N10 sing Y N 220 IPY C26 H26 sing N N 221 IPY C27 N9 sing Y N 222 IPY C27 H27 sing N N 223 IPY C28 N9 sing N N 224 IPY C28 H281 sing N N 225 IPY C28 H282 sing N N 226 IPY C28 H283 sing N N 227 IPY C29 C30 sing N N 228 IPY C29 N11 sing N N 229 IPY C29 H291 sing N N 230 IPY C29 H292 sing N N 231 IPY C30 C31 sing N N 232 IPY C30 H301 sing N N 233 IPY C30 H302 sing N N 234 IPY C31 O5 doub N N 235 IPY C31 N6 sing N N 236 IPY C32 H32 sing N N 237 IPY N1 HN1 sing N N 238 IPY N4 HN4 sing N N 239 IPY N6 HN6 sing N N 240 IPY N7 HN7 sing N N 241 IPY N8 HN8 sing N N 242 IPY N11 H11 sing N N 243 # _ndb_struct_conf_na.entry_id 408D _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 B DG 10 1_555 1.561 0.208 0.175 -0.397 -22.538 14.659 1 A_DC1:DG20_B A 1 ? B 20 ? ? 1 1 A DC 2 1_555 B DG 9 1_555 -0.199 0.374 -0.368 -3.259 -11.599 9.201 2 A_DC2:DG19_B A 2 ? B 19 ? ? 1 1 A DA 3 1_555 B DT 8 1_555 -0.018 -0.347 0.129 -3.157 -8.107 2.087 3 A_DA3:DT18_B A 3 ? B 18 ? 20 1 1 A DG 4 1_555 B DC 7 1_555 -0.744 -0.510 0.172 -8.833 0.795 -2.009 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 1 A DT 5 1_555 B DA 6 1_555 0.024 -0.381 0.177 -2.988 -16.669 -10.809 5 A_DT5:DA16_B A 5 ? B 16 ? 20 1 1 A DA 6 1_555 B DT 5 1_555 0.072 0.182 -0.030 -0.021 -17.065 -8.258 6 A_DA6:DT15_B A 6 ? B 15 ? 20 1 1 A DC 7 1_555 B DG 4 1_555 0.089 -0.038 -0.044 2.435 -4.785 1.027 7 A_DC7:DG14_B A 7 ? B 14 ? 19 1 1 A DT 8 1_555 B DA 3 1_555 -0.240 -0.499 0.127 -4.602 -7.668 2.337 8 A_DT8:DA13_B A 8 ? B 13 ? 20 1 1 A DG 9 1_555 B DC 2 1_555 -0.084 -0.284 -0.092 -0.204 -8.280 3.965 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DG 10 1_555 B DC 1 1_555 -0.344 0.295 0.282 8.080 -13.150 10.929 10 A_DG10:DC11_B A 10 ? B 11 ? ? 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 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 -0.519 0.938 3.084 3.055 10.992 28.695 -0.353 1.565 3.152 21.152 -5.879 30.836 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DA 3 1_555 B DT 8 1_555 0.034 1.193 3.402 -3.922 7.079 38.975 0.872 -0.539 3.537 10.473 5.802 39.774 2 AA_DC2DA3:DT18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DA 3 1_555 B DT 8 1_555 A DG 4 1_555 B DC 7 1_555 -1.295 0.098 3.455 -5.416 12.873 30.409 -2.175 1.267 3.396 23.075 9.709 33.394 3 AA_DA3DG4:DC17DT18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DG 4 1_555 B DC 7 1_555 A DT 5 1_555 B DA 6 1_555 -1.317 0.119 3.216 -1.198 3.479 37.270 -0.267 1.896 3.253 5.427 1.869 37.445 4 AA_DG4DT5:DA16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DT 5 1_555 B DA 6 1_555 A DA 6 1_555 B DT 5 1_555 0.134 0.499 3.199 1.980 -4.156 34.563 1.445 0.068 3.123 -6.956 -3.314 34.859 5 AA_DT5DA6:DT15DA16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DA 6 1_555 B DT 5 1_555 A DC 7 1_555 B DG 4 1_555 1.544 0.261 3.338 0.725 3.608 35.797 -0.106 -2.393 3.377 5.851 -1.176 35.979 6 AA_DA6DC7:DG14DT15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DC 7 1_555 B DG 4 1_555 A DT 8 1_555 B DA 3 1_555 1.242 0.247 3.327 5.921 13.898 32.125 -1.782 -1.109 3.323 23.558 -10.036 35.414 7 AA_DC7DT8:DA13DG14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DT 8 1_555 B DA 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.078 1.702 3.338 0.076 3.804 40.157 2.021 0.123 3.478 5.525 -0.111 40.329 8 AA_DT8DG9:DC12DA13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DG 10 1_555 B DC 1 1_555 -0.174 0.596 3.092 -2.162 9.141 31.470 -0.474 -0.053 3.142 16.402 3.879 32.808 9 AA_DG9DG10:DC11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 408D _atom_sites.fract_transf_matrix[1][1] 0.016485 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.010949 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033113 _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] 0.027622 _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_