data_407D # _entry.id 407D # _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 407D pdb_0000407d 10.2210/pdb407d/pdb RCSB BDD002 ? ? WWPDB D_1000179207 ? ? # 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 2011-11-16 5 'Structure model' 1 4 2017-05-03 6 'Structure model' 2 0 2018-09-26 7 'Structure model' 2 1 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' 'Atomic model' 4 5 'Structure model' 'Source and taxonomy' 5 5 'Structure model' 'Structure summary' 6 6 'Structure model' Advisory 7 6 'Structure model' 'Data collection' 8 6 'Structure model' 'Derived calculations' 9 6 'Structure model' 'Non-polymer description' 10 6 'Structure model' 'Structure summary' 11 7 'Structure model' 'Data collection' 12 7 'Structure model' 'Database references' 13 7 '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 6 'Structure model' chem_comp 2 6 'Structure model' entity 3 6 'Structure model' ndb_struct_na_base_pair 4 6 'Structure model' pdbx_distant_solvent_atoms 5 6 'Structure model' pdbx_entity_nonpoly 6 6 'Structure model' struct_conn 7 7 'Structure model' chem_comp_atom 8 7 'Structure model' chem_comp_bond 9 7 'Structure model' database_2 10 7 '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 6 'Structure model' '_chem_comp.formula' 2 6 'Structure model' '_chem_comp.formula_weight' 3 6 'Structure model' '_chem_comp.name' 4 6 'Structure model' '_entity.formula_weight' 5 6 'Structure model' '_entity.pdbx_description' 6 6 'Structure model' '_ndb_struct_na_base_pair.hbond_type_12' 7 6 'Structure model' '_ndb_struct_na_base_pair.hbond_type_28' 8 6 'Structure model' '_pdbx_entity_nonpoly.name' 9 6 'Structure model' '_struct_conn.details' 10 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 11 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 12 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 13 6 'Structure model' '_struct_conn.ptnr1_label_comp_id' 14 6 'Structure model' '_struct_conn.ptnr1_label_seq_id' 15 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 6 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 6 'Structure model' '_struct_conn.ptnr2_label_seq_id' 20 7 'Structure model' '_database_2.pdbx_DOI' 21 7 'Structure model' '_database_2.pdbx_database_accession' 22 7 'Structure model' '_struct_site.pdbx_auth_asym_id' 23 7 'Structure model' '_struct_site.pdbx_auth_comp_id' 24 7 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 407D _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.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Rees, D.C.' _audit_author.pdbx_ordinal 1 _audit_author.identifier_ORCID ? # _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 syn ;DNA (5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3') ; 3045.004 2 ? ? ? ? 2 non-polymer syn ;~{N}-[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-4-oxidanyl-pyrrol-3-yl]-1-methyl-imidazole-2-carboxamide ; 663.727 2 ? ? ? ? 3 non-polymer syn 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 122.143 1 ? ? ? ? 4 water nat water 18.015 65 ? ? ? ? # _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 ;~{N}-[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-4-oxidanyl-pyrrol-3-yl]-1-methyl-imidazole-2-carboxamide ; HP1 3 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL TRS 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 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 # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 HP1 non-polymer . ;~{N}-[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-4-oxidanyl-pyrrol-3-yl]-1-methyl-imidazole-2-carboxamide ; 'IMIDAZOLE-HYDROXYPYRROLE-PYRROLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE' 'C31 H41 N11 O6' 663.727 TRS non-polymer . 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 'TRIS BUFFER' 'C4 H12 N O3 1' 122.143 # 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 HP1 1 22 22 HP1 HP1 A . D 3 TRS 1 200 200 TRS TRS A . E 2 HP1 1 21 21 HP1 HP1 B . F 4 HOH 1 23 23 HOH HOH A . F 4 HOH 2 30 30 HOH HOH A . F 4 HOH 3 31 31 HOH HOH A . F 4 HOH 4 32 32 HOH HOH A . F 4 HOH 5 33 33 HOH HOH A . F 4 HOH 6 34 34 HOH HOH A . F 4 HOH 7 35 35 HOH HOH A . F 4 HOH 8 38 38 HOH HOH A . F 4 HOH 9 39 39 HOH HOH A . F 4 HOH 10 40 40 HOH HOH A . F 4 HOH 11 43 43 HOH HOH A . F 4 HOH 12 44 44 HOH HOH A . F 4 HOH 13 46 46 HOH HOH A . F 4 HOH 14 48 48 HOH HOH A . F 4 HOH 15 50 50 HOH HOH A . F 4 HOH 16 52 52 HOH HOH A . F 4 HOH 17 56 56 HOH HOH A . F 4 HOH 18 59 59 HOH HOH A . F 4 HOH 19 60 60 HOH HOH A . F 4 HOH 20 61 61 HOH HOH A . F 4 HOH 21 64 64 HOH HOH A . F 4 HOH 22 67 67 HOH HOH A . F 4 HOH 23 70 70 HOH HOH A . F 4 HOH 24 75 75 HOH HOH A . F 4 HOH 25 76 76 HOH HOH A . F 4 HOH 26 77 77 HOH HOH A . F 4 HOH 27 78 78 HOH HOH A . F 4 HOH 28 81 81 HOH HOH A . F 4 HOH 29 83 83 HOH HOH A . F 4 HOH 30 88 88 HOH HOH A . F 4 HOH 31 89 89 HOH HOH A . F 4 HOH 32 91 91 HOH HOH A . F 4 HOH 33 93 93 HOH HOH A . F 4 HOH 34 95 95 HOH HOH A . F 4 HOH 35 100 100 HOH HOH A . F 4 HOH 36 107 107 HOH HOH A . G 4 HOH 1 26 26 HOH HOH B . G 4 HOH 2 27 27 HOH HOH B . G 4 HOH 3 28 28 HOH HOH B . G 4 HOH 4 29 29 HOH HOH B . G 4 HOH 5 37 37 HOH HOH B . G 4 HOH 6 41 41 HOH HOH B . G 4 HOH 7 42 42 HOH HOH B . G 4 HOH 8 47 47 HOH HOH B . G 4 HOH 9 49 49 HOH HOH B . G 4 HOH 10 51 51 HOH HOH B . G 4 HOH 11 53 53 HOH HOH B . G 4 HOH 12 54 54 HOH HOH B . G 4 HOH 13 55 55 HOH HOH B . G 4 HOH 14 57 57 HOH HOH B . G 4 HOH 15 62 62 HOH HOH B . G 4 HOH 16 63 63 HOH HOH B . G 4 HOH 17 65 65 HOH HOH B . G 4 HOH 18 68 68 HOH HOH B . G 4 HOH 19 69 69 HOH HOH B . G 4 HOH 20 72 72 HOH HOH B . G 4 HOH 21 74 74 HOH HOH B . G 4 HOH 22 82 82 HOH HOH B . G 4 HOH 23 85 85 HOH HOH B . G 4 HOH 24 86 86 HOH HOH B . G 4 HOH 25 90 90 HOH HOH B . G 4 HOH 26 104 104 HOH HOH B . G 4 HOH 27 105 105 HOH HOH B . G 4 HOH 28 109 109 HOH HOH B . G 4 HOH 29 112 112 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 407D _cell.length_a 60.440 _cell.length_b 30.510 _cell.length_c 42.760 _cell.angle_alpha 90.00 _cell.angle_beta 120.47 _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 407D _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 _symmetry.space_group_name_Hall ? # _exptl.entry_id 407D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.68 _exptl_crystal.density_percent_sol 54.06 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _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 MARRESEARCH _diffrn_detector.pdbx_collection_date 1997-12-15 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL9-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL9-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 407D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F 0.000 _reflns.d_resolution_low 17.000 _reflns.d_resolution_high 2.200 _reflns.number_obs 3070 _reflns.number_all 3070 _reflns.percent_possible_obs 91.500 _reflns.pdbx_Rmerge_I_obs 0.0300000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.200 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 407D _refine.ls_number_reflns_obs 3056 _refine.ls_number_reflns_all 3224 _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 2.200 _refine.ls_percent_reflns_obs 91.600 _refine.ls_R_factor_obs 0.2100000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2100000 _refine.ls_R_factor_R_free 0.2360000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.800 _refine.ls_number_reflns_R_free 168 _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.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _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 404 _refine_hist.pdbx_number_atoms_ligand 124 _refine_hist.number_atoms_solvent 65 _refine_hist.number_atoms_total 593 _refine_hist.d_res_high 2.200 _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 0.016 ? ? ? '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 2.17 ? ? ? '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 IPP_NODIH.PAR _pdbx_xplor_file.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 407D _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 407D _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 407D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DRUGS 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 3 ? E N N 2 ? F N N 4 ? G N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 407D _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code CCAGTACTGG _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession 407D _struct_ref.pdbx_db_isoform ? # 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 407D A 1 ? 10 ? 407D 1 ? 10 ? 1 10 2 1 407D B 1 ? 10 ? 407D 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,G # _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 # 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 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 8 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 8 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B HP1 21 ? 17 'BINDING SITE FOR RESIDUE HP1 B 21' AC2 Software A HP1 22 ? 17 'BINDING SITE FOR RESIDUE HP1 A 22' AC3 Software A TRS 200 ? 5 'BINDING SITE FOR RESIDUE TRS A 200' 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 DC A 2 ? DC A 2 . ? 1_555 ? 2 AC1 17 DA A 3 ? DA A 3 . ? 1_555 ? 3 AC1 17 DG A 4 ? DG A 4 . ? 1_555 ? 4 AC1 17 DA A 6 ? DA A 6 . ? 1_555 ? 5 AC1 17 HP1 C . ? HP1 A 22 . ? 1_555 ? 6 AC1 17 DC B 1 ? DC B 11 . ? 2_656 ? 7 AC1 17 DG B 4 ? DG B 14 . ? 1_555 ? 8 AC1 17 DT B 5 ? DT B 15 . ? 1_555 ? 9 AC1 17 DA B 6 ? DA B 16 . ? 1_555 ? 10 AC1 17 DC B 7 ? DC B 17 . ? 1_555 ? 11 AC1 17 DT B 8 ? DT B 18 . ? 4_556 ? 12 AC1 17 DT B 8 ? DT B 18 . ? 1_555 ? 13 AC1 17 DG B 9 ? DG B 19 . ? 1_555 ? 14 AC1 17 DG B 10 ? DG B 20 . ? 1_555 ? 15 AC1 17 DG B 10 ? DG B 20 . ? 4_546 ? 16 AC1 17 HOH G . ? HOH B 68 . ? 1_555 ? 17 AC1 17 HOH G . ? HOH B 105 . ? 1_555 ? 18 AC2 17 DC A 1 ? DC A 1 . ? 4_545 ? 19 AC2 17 DC A 2 ? DC A 2 . ? 4_545 ? 20 AC2 17 DG A 4 ? DG A 4 . ? 1_555 ? 21 AC2 17 DT A 5 ? DT A 5 . ? 1_555 ? 22 AC2 17 DA A 6 ? DA A 6 . ? 1_555 ? 23 AC2 17 DC A 7 ? DC A 7 . ? 1_555 ? 24 AC2 17 DT A 8 ? DT A 8 . ? 1_555 ? 25 AC2 17 DG A 9 ? DG A 9 . ? 1_555 ? 26 AC2 17 HOH F . ? HOH A 52 . ? 1_555 ? 27 AC2 17 HOH F . ? HOH A 75 . ? 1_555 ? 28 AC2 17 DC B 1 ? DC B 11 . ? 2_656 ? 29 AC2 17 DC B 2 ? DC B 12 . ? 2_656 ? 30 AC2 17 DA B 3 ? DA B 13 . ? 1_555 ? 31 AC2 17 DG B 4 ? DG B 14 . ? 1_555 ? 32 AC2 17 DA B 6 ? DA B 16 . ? 1_555 ? 33 AC2 17 DG B 10 ? DG B 20 . ? 4_546 ? 34 AC2 17 HP1 E . ? HP1 B 21 . ? 1_555 ? 35 AC3 5 DT A 5 ? DT A 5 . ? 1_555 ? 36 AC3 5 DA A 6 ? DA A 6 . ? 1_555 ? 37 AC3 5 HOH F . ? HOH A 34 . ? 1_555 ? 38 AC3 5 HOH F . ? HOH A 59 . ? 1_555 ? 39 AC3 5 DG B 4 ? DG B 14 . ? 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 OP2 A DC 2 ? ? O A HOH 35 ? ? 1.97 2 1 O B HOH 26 ? ? O B HOH 62 ? ? 2.15 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O6 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 DG _pdbx_validate_symm_contact.auth_seq_id_1 10 _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 26 _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 2.16 # 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 "C3'" B DG 14 ? ? "C2'" B DG 14 ? ? "C1'" B DG 14 ? ? 97.51 102.40 -4.89 0.80 N 2 1 "C3'" B DT 15 ? ? "C2'" B DT 15 ? ? "C1'" B DT 15 ? ? 94.56 102.40 -7.84 0.80 N 3 1 "O4'" B DT 15 ? ? "C1'" B DT 15 ? ? N1 B DT 15 ? ? 110.93 108.30 2.63 0.30 N 4 1 C6 B DT 15 ? ? N1 B DT 15 ? ? "C1'" B DT 15 ? ? 100.15 120.40 -20.25 1.50 N 5 1 C2 B DT 15 ? ? N1 B DT 15 ? ? "C1'" B DT 15 ? ? 137.27 118.20 19.07 1.60 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 ? ? 0.074 'SIDE CHAIN' 2 1 DG A 10 ? ? 0.066 'SIDE CHAIN' 3 1 DG B 14 ? ? 0.065 'SIDE CHAIN' 4 1 DA B 16 ? ? 0.067 'SIDE CHAIN' # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR 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 HOH _pdbx_struct_special_symmetry.auth_seq_id 60 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id F _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 89 ? 7.98 . 2 1 O ? B HOH 90 ? 6.96 . 3 1 O ? B HOH 104 ? 6.56 . 4 1 O ? B HOH 112 ? . 6.62 # 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 HP1 C C Y N 147 HP1 C1 C Y N 148 HP1 C2 C Y N 149 HP1 C3 C N N 150 HP1 C4 C Y N 151 HP1 C5 C N N 152 HP1 C6 C Y N 153 HP1 C8 C Y N 154 HP1 C9 C N N 155 HP1 C10 C Y N 156 HP1 C11 C N N 157 HP1 C12 C Y N 158 HP1 C13 C Y N 159 HP1 C14 C Y N 160 HP1 C15 C N N 161 HP1 C16 C Y N 162 HP1 C18 C N N 163 HP1 C19 C N N 164 HP1 C20 C N N 165 HP1 C21 C N N 166 HP1 C22 C N N 167 HP1 C23 C N N 168 HP1 C24 C N N 169 HP1 C25 C Y N 170 HP1 C26 C Y N 171 HP1 C27 C Y N 172 HP1 C28 C N N 173 HP1 C29 C N N 174 HP1 C30 C N N 175 HP1 C31 C N N 176 HP1 C32 C Y N 177 HP1 O1 O N N 178 HP1 O2 O N N 179 HP1 O3 O N N 180 HP1 O4 O N N 181 HP1 O5 O N N 182 HP1 O6 O N N 183 HP1 N N Y N 184 HP1 N1 N N N 185 HP1 N3 N Y N 186 HP1 N4 N N N 187 HP1 N5 N Y N 188 HP1 N6 N N N 189 HP1 N7 N N N 190 HP1 N8 N N N 191 HP1 N9 N Y N 192 HP1 N10 N Y N 193 HP1 N11 N N N 194 HP1 H1 H N N 195 HP1 H2 H N N 196 HP1 H3 H N N 197 HP1 H4 H N N 198 HP1 H5 H N N 199 HP1 H6 H N N 200 HP1 H7 H N N 201 HP1 H8 H N N 202 HP1 H9 H N N 203 HP1 H10 H N N 204 HP1 H11 H N N 205 HP1 H12 H N N 206 HP1 H13 H N N 207 HP1 H14 H N N 208 HP1 H15 H N N 209 HP1 H16 H N N 210 HP1 H17 H N N 211 HP1 H18 H N N 212 HP1 H19 H N N 213 HP1 H20 H N N 214 HP1 H21 H N N 215 HP1 H22 H N N 216 HP1 H23 H N N 217 HP1 H24 H N N 218 HP1 H25 H N N 219 HP1 H26 H N N 220 HP1 H27 H N N 221 HP1 H28 H N N 222 HP1 H29 H N N 223 HP1 H30 H N N 224 HP1 H31 H N N 225 HP1 H32 H N N 226 HP1 H33 H N N 227 HP1 H34 H N N 228 HP1 H35 H N N 229 HP1 H36 H N N 230 HP1 H37 H N N 231 HP1 H38 H N N 232 HP1 H39 H N N 233 HP1 H41 H N N 234 HP1 H42 H N N 235 TRS C C N N 236 TRS C1 C N N 237 TRS C2 C N N 238 TRS C3 C N N 239 TRS N N N N 240 TRS O1 O N N 241 TRS O2 O N N 242 TRS O3 O N N 243 TRS H11 H N N 244 TRS H12 H N N 245 TRS H21 H N N 246 TRS H22 H N N 247 TRS H31 H N N 248 TRS H32 H N N 249 TRS HN1 H N N 250 TRS HN2 H N N 251 TRS HN3 H N N 252 TRS HO1 H N N 253 TRS HO2 H N N 254 TRS HO3 H N N 255 # 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 HP1 C22 N7 sing N N 152 HP1 N7 C20 sing N N 153 HP1 N7 C21 sing N N 154 HP1 C20 C19 sing N N 155 HP1 O5 C31 doub N N 156 HP1 C19 C18 sing N N 157 HP1 C18 N6 sing N N 158 HP1 C31 N6 sing N N 159 HP1 C31 C30 sing N N 160 HP1 O3 C23 doub N N 161 HP1 C15 N5 sing N N 162 HP1 C29 C30 sing N N 163 HP1 C29 N11 sing N N 164 HP1 C23 N11 sing N N 165 HP1 C23 C16 sing N N 166 HP1 N5 C16 sing Y N 167 HP1 N5 C14 sing Y N 168 HP1 C16 C13 doub Y N 169 HP1 C14 C12 doub Y N 170 HP1 C13 C12 sing Y N 171 HP1 C12 N4 sing N N 172 HP1 O2 C11 doub N N 173 HP1 N4 C11 sing N N 174 HP1 C11 C10 sing N N 175 HP1 C10 N3 sing Y N 176 HP1 C10 C1 doub Y N 177 HP1 C9 N3 sing N N 178 HP1 N3 C8 sing Y N 179 HP1 C1 C6 sing Y N 180 HP1 C8 C6 doub Y N 181 HP1 C6 N1 sing N N 182 HP1 N1 C5 sing N N 183 HP1 O6 C32 sing N N 184 HP1 C5 O1 doub N N 185 HP1 C5 C4 sing N N 186 HP1 C32 C4 doub Y N 187 HP1 C32 C sing Y N 188 HP1 C4 N sing Y N 189 HP1 C N8 sing N N 190 HP1 C C2 doub Y N 191 HP1 N8 C24 sing N N 192 HP1 N10 C26 sing Y N 193 HP1 N10 C25 doub Y N 194 HP1 N C2 sing Y N 195 HP1 N C3 sing N N 196 HP1 C26 C27 doub Y N 197 HP1 C24 C25 sing N N 198 HP1 C24 O4 doub N N 199 HP1 C25 N9 sing Y N 200 HP1 C27 N9 sing Y N 201 HP1 N9 C28 sing N N 202 HP1 C1 H1 sing N N 203 HP1 C2 H2 sing N N 204 HP1 C3 H3 sing N N 205 HP1 C3 H4 sing N N 206 HP1 C3 H5 sing N N 207 HP1 C8 H6 sing N N 208 HP1 C9 H7 sing N N 209 HP1 C9 H8 sing N N 210 HP1 C9 H9 sing N N 211 HP1 C13 H10 sing N N 212 HP1 C14 H11 sing N N 213 HP1 C15 H12 sing N N 214 HP1 C15 H13 sing N N 215 HP1 C15 H14 sing N N 216 HP1 C18 H15 sing N N 217 HP1 C18 H16 sing N N 218 HP1 C19 H17 sing N N 219 HP1 C19 H18 sing N N 220 HP1 C20 H19 sing N N 221 HP1 C20 H20 sing N N 222 HP1 C21 H21 sing N N 223 HP1 C21 H22 sing N N 224 HP1 C21 H23 sing N N 225 HP1 C22 H24 sing N N 226 HP1 C22 H25 sing N N 227 HP1 C22 H26 sing N N 228 HP1 C26 H27 sing N N 229 HP1 C27 H28 sing N N 230 HP1 C28 H29 sing N N 231 HP1 C28 H30 sing N N 232 HP1 C28 H31 sing N N 233 HP1 C29 H32 sing N N 234 HP1 C29 H33 sing N N 235 HP1 C30 H34 sing N N 236 HP1 C30 H35 sing N N 237 HP1 O6 H36 sing N N 238 HP1 N1 H37 sing N N 239 HP1 N4 H38 sing N N 240 HP1 N6 H39 sing N N 241 HP1 N8 H41 sing N N 242 HP1 N11 H42 sing N N 243 TRS C C1 sing N N 244 TRS C C2 sing N N 245 TRS C C3 sing N N 246 TRS C N sing N N 247 TRS C1 O1 sing N N 248 TRS C1 H11 sing N N 249 TRS C1 H12 sing N N 250 TRS C2 O2 sing N N 251 TRS C2 H21 sing N N 252 TRS C2 H22 sing N N 253 TRS C3 O3 sing N N 254 TRS C3 H31 sing N N 255 TRS C3 H32 sing N N 256 TRS N HN1 sing N N 257 TRS N HN2 sing N N 258 TRS N HN3 sing N N 259 TRS O1 HO1 sing N N 260 TRS O2 HO2 sing N N 261 TRS O3 HO3 sing N N 262 # _ndb_struct_conf_na.entry_id 407D _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 -0.092 0.016 -0.388 5.892 -24.243 6.860 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 -0.933 0.132 0.063 -15.405 -6.495 1.297 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DA 3 1_555 B DT 8 1_555 -0.195 -0.233 -0.282 -5.046 -14.127 1.418 3 A_DA3:DT18_B A 3 ? B 18 ? 20 1 1 A DG 4 1_555 B DC 7 1_555 -0.753 -0.268 0.078 -3.268 -3.302 3.008 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 1 A DT 5 1_555 B DA 6 1_555 0.019 0.289 0.226 0.737 -12.306 -5.022 5 A_DT5:DA16_B A 5 ? B 16 ? 20 1 1 A DA 6 1_555 B DT 5 1_555 0.408 0.381 1.220 7.291 -15.673 -4.289 6 A_DA6:DT15_B A 6 ? B 15 ? 20 1 1 A DC 7 1_555 B DG 4 1_555 -0.084 -0.287 0.444 -1.129 -6.284 -3.265 7 A_DC7:DG14_B A 7 ? B 14 ? 19 1 1 A DT 8 1_555 B DA 3 1_555 0.240 -0.373 0.146 0.838 -10.237 -2.783 8 A_DT8:DA13_B A 8 ? B 13 ? 20 1 1 A DG 9 1_555 B DC 2 1_555 -0.452 0.004 0.492 0.172 -6.787 8.132 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DG 10 1_555 B DC 1 1_555 0.425 -0.198 0.735 16.224 -12.075 5.705 10 A_DG10:DC11_B A 10 ? B 11 ? 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 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.243 0.148 3.732 -1.090 12.940 35.662 -1.683 -0.535 3.563 20.317 1.711 37.881 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 -0.029 1.057 3.175 0.585 1.625 40.445 1.350 0.106 3.213 2.350 -0.846 40.481 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 -0.853 0.383 3.161 -4.572 13.051 28.821 -1.711 0.708 3.135 24.517 8.589 31.904 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 -1.075 0.303 3.230 -2.013 -0.075 34.536 0.521 1.499 3.285 -0.126 3.387 34.593 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 0.168 -0.037 3.014 -4.737 1.516 35.588 -0.258 -0.894 2.964 2.466 7.703 35.923 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 0.992 0.583 3.685 4.800 -0.494 38.862 0.939 -0.822 3.769 -0.739 -7.181 39.149 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 0.420 -0.274 3.516 4.413 11.837 30.125 -2.694 0.074 3.213 21.618 -8.059 32.610 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 0.453 2.465 3.376 -2.046 -0.146 45.352 3.207 -0.773 3.346 -0.189 2.652 45.396 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 0.273 0.556 2.959 -2.588 9.881 30.400 -0.649 -0.928 2.958 18.209 4.769 32.032 9 AA_DG9DG10:DC11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 407D _atom_sites.fract_transf_matrix[1][1] 0.016545 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009734 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.032776 _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] 0.027134 _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_