data_334D # _entry.id 334D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 334D pdb_0000334d 10.2210/pdb334d/pdb RCSB GDJ054 ? ? WWPDB D_1000178803 ? ? # 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 1997-08-29 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-04-04 5 'Structure model' 1 4 2024-02-21 6 'Structure model' 1 5 2024-04-03 # _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 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 'Structure model' 'Refinement description' # 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' diffrn_source 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_site 8 6 'Structure model' pdbx_initial_refinement_model # 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' '_diffrn_source.type' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.value' 17 5 'Structure model' '_struct_conn.pdbx_dist_value' 18 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 19 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 20 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 22 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 23 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 24 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 25 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 26 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 27 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 28 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 29 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 30 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 31 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 32 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 334D _pdbx_database_status.recvd_initial_deposition_date 1997-05-22 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kopka, M.L.' 1 'Goodsell, D.S.' 2 'Dickerson, R.E.' 3 # _citation.id primary _citation.title 'Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G.' _citation.journal_abbrev Structure _citation.journal_volume 5 _citation.page_first 1033 _citation.page_last 1046 _citation.year 1997 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9309219 _citation.pdbx_database_id_DOI '10.1016/S0969-2126(97)00255-4' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kopka, M.L.' 1 ? primary 'Goodsell, D.S.' 2 ? primary 'Han, G.W.' 3 ? primary 'Chiu, T.K.' 4 ? primary 'Lown, J.W.' 5 ? primary 'Dickerson, R.E.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*AP*TP*GP*GP*CP*CP*AP*TP*G)-3') ; 3045.004 2 ? ? ? ? 2 non-polymer syn 'DIIMIDAZOLE LEXITROPSIN' 362.367 2 ? ? ? ? 3 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 4 water nat water 18.015 62 ? ? ? ? # _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)(DA)(DT)(DG)(DG)(DC)(DC)(DA)(DT)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CATGGCCATG _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 'DIIMIDAZOLE LEXITROPSIN' DIM 3 'CALCIUM ION' CA 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 DA n 1 3 DT n 1 4 DG n 1 5 DG n 1 6 DC n 1 7 DC n 1 8 DA n 1 9 DT 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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 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 DIM non-polymer . 'DIIMIDAZOLE LEXITROPSIN' ? 'C14 H20 N9 O3 1' 362.367 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DA 2 2 2 DA A A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DT 9 9 9 DT T 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 DA 2 12 12 DA A B . n B 1 3 DT 3 13 13 DT T B . n B 1 4 DG 4 14 14 DG G B . n B 1 5 DG 5 15 15 DG G B . n B 1 6 DC 6 16 16 DC C B . n B 1 7 DC 7 17 17 DC C B . n B 1 8 DA 8 18 18 DA A B . n B 1 9 DT 9 19 19 DT T 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 DIM 1 21 21 DIM DIM A . D 3 CA 1 23 23 CA OC4 A . E 2 DIM 1 22 22 DIM DIM B . F 4 HOH 1 24 24 HOH HOH A . F 4 HOH 2 26 26 HOH HOH A . F 4 HOH 3 28 28 HOH HOH A . F 4 HOH 4 34 34 HOH HOH A . F 4 HOH 5 35 35 HOH HOH A . F 4 HOH 6 36 36 HOH HOH A . F 4 HOH 7 37 37 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 41 41 HOH HOH A . F 4 HOH 12 42 42 HOH HOH A . F 4 HOH 13 45 45 HOH HOH A . F 4 HOH 14 46 46 HOH HOH A . F 4 HOH 15 48 48 HOH HOH A . F 4 HOH 16 49 49 HOH HOH A . F 4 HOH 17 54 54 HOH HOH A . F 4 HOH 18 56 56 HOH HOH A . F 4 HOH 19 58 58 HOH HOH A . F 4 HOH 20 59 59 HOH HOH A . F 4 HOH 21 60 60 HOH HOH A . F 4 HOH 22 63 63 HOH HOH A . F 4 HOH 23 64 64 HOH HOH A . F 4 HOH 24 65 65 HOH HOH A . F 4 HOH 25 66 66 HOH HOH A . F 4 HOH 26 67 67 HOH HOH A . F 4 HOH 27 69 69 HOH HOH A . F 4 HOH 28 71 71 HOH HOH A . F 4 HOH 29 73 73 HOH HOH A . F 4 HOH 30 75 75 HOH HOH A . F 4 HOH 31 76 76 HOH HOH A . F 4 HOH 32 80 80 HOH HOH A . F 4 HOH 33 82 23 HOH OC4 A . F 4 HOH 34 83 23 HOH OC4 A . F 4 HOH 35 84 23 HOH OC4 A . F 4 HOH 36 85 23 HOH OC4 A . G 4 HOH 1 25 25 HOH HOH B . G 4 HOH 2 27 27 HOH HOH B . G 4 HOH 3 29 29 HOH HOH B . G 4 HOH 4 30 30 HOH HOH B . G 4 HOH 5 31 31 HOH HOH B . G 4 HOH 6 32 32 HOH HOH B . G 4 HOH 7 33 33 HOH HOH B . G 4 HOH 8 43 43 HOH HOH B . G 4 HOH 9 44 44 HOH HOH B . G 4 HOH 10 47 47 HOH HOH B . G 4 HOH 11 50 50 HOH HOH B . G 4 HOH 12 51 51 HOH HOH B . G 4 HOH 13 52 52 HOH HOH B . G 4 HOH 14 53 53 HOH HOH B . G 4 HOH 15 55 55 HOH HOH B . G 4 HOH 16 57 57 HOH HOH B . G 4 HOH 17 61 61 HOH HOH B . G 4 HOH 18 62 62 HOH HOH B . G 4 HOH 19 68 68 HOH HOH B . G 4 HOH 20 70 70 HOH HOH B . G 4 HOH 21 72 72 HOH HOH B . G 4 HOH 22 74 74 HOH HOH B . G 4 HOH 23 77 77 HOH HOH B . G 4 HOH 24 78 78 HOH HOH B . G 4 HOH 25 79 79 HOH HOH B . G 4 HOH 26 81 81 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 NUCLSQ refinement . ? 2 MSC 'data reduction' . ? 3 MSC 'data scaling' . ? 4 X-PLOR phasing . ? 5 # _cell.entry_id 334D _cell.length_a 36.654 _cell.length_b 42.643 _cell.length_c 34.684 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 334D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _exptl.entry_id 334D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.14 _exptl_crystal.density_percent_sol 50.0000 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.40 _exptl_crystal_grow.pdbx_details 'pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 CACL2 ? ? ? 1 4 1 SPERMINE_HCL ? ? ? 1 5 2 WATER ? ? ? 1 6 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 278.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS II' _diffrn_detector.pdbx_collection_date 1993-09-15 _diffrn_detector.details 'MIRROR MSC-YALE' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 334D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 8.000 _reflns.d_resolution_high 1.800 _reflns.number_obs 4895 _reflns.number_all ? _reflns.percent_possible_obs 93.000 _reflns.pdbx_Rmerge_I_obs 0.0374000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 21.41 _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.800 _reflns_shell.d_res_low 1.850 _reflns_shell.percent_possible_all 91.90 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 334D _refine.ls_number_reflns_obs 4895 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 1.800 _refine.ls_percent_reflns_obs 92.000 _refine.ls_R_factor_obs 0.2000000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2000000 _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'AN IDEAL HELIX RMS FIT TO BDJ057' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _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 57 _refine_hist.number_atoms_solvent 58 _refine_hist.number_atoms_total 519 _refine_hist.d_res_high 1.800 _refine_hist.d_res_low 8.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function n_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_planar_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_it 4.026 6.000 ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it 4.664 6.000 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it 4.858 6.000 ? ? 'X-RAY DIFFRACTION' ? n_phos_angle_it 4.654 6.000 ? ? 'X-RAY DIFFRACTION' ? n_bond_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_dihedral_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_impr_tor ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_d 0.026 0.030 ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d 0.039 0.027 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d 0.050 0.040 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d 0.069 0.050 ? ? 'X-RAY DIFFRACTION' ? n_plane_restr 0.016 0.020 ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr 0.146 0.150 ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd 0.085 0.100 ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd 0.104 0.100 ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 334D _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 334D _struct.title 'DEFINING GC-SPECIFICITY IN THE MINOR GROOVE: SIDE-BY-SIDE BINDING OF THE DI-IMIDAZOLE LEXITROPSIN TO C-A-T-G-G-C-C-A-T-G' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 334D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, 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.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 334D _struct_ref.pdbx_db_accession 334D _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 334D A 1 ? 10 ? 334D 1 ? 10 ? 1 10 2 1 334D B 1 ? 10 ? 334D 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 # _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 metalc1 metalc ? ? A DA 8 OP2 ? ? ? 1_555 D CA . CA ? ? A DA 8 A CA 23 1_555 ? ? ? ? ? ? ? 2.917 ? ? metalc2 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 23 A HOH 82 1_555 ? ? ? ? ? ? ? 2.594 ? ? metalc3 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 23 A HOH 83 1_555 ? ? ? ? ? ? ? 2.553 ? ? metalc4 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 23 A HOH 84 1_555 ? ? ? ? ? ? ? 2.524 ? ? metalc5 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 23 A HOH 85 1_555 ? ? ? ? ? ? ? 2.479 ? ? metalc6 metalc ? ? D CA . CA ? ? ? 1_555 B DG 4 OP1 ? ? A CA 23 B DG 14 4_556 ? ? ? ? ? ? ? 2.342 ? ? 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 DA 2 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 2 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 2 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 8 N1 ? ? A DT 3 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 8 N6 ? ? A DT 3 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 6 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 6 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 6 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 8 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 8 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 9 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 9 B DA 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 ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP2 ? A DA 8 ? A DA 8 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 82 ? 1_555 80.5 ? 2 OP2 ? A DA 8 ? A DA 8 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 83 ? 1_555 87.2 ? 3 O ? F HOH . ? A HOH 82 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 83 ? 1_555 68.0 ? 4 OP2 ? A DA 8 ? A DA 8 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 84 ? 1_555 82.2 ? 5 O ? F HOH . ? A HOH 82 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 84 ? 1_555 79.0 ? 6 O ? F HOH . ? A HOH 83 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 84 ? 1_555 146.6 ? 7 OP2 ? A DA 8 ? A DA 8 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 85 ? 1_555 85.3 ? 8 O ? F HOH . ? A HOH 82 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 85 ? 1_555 165.8 ? 9 O ? F HOH . ? A HOH 83 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 85 ? 1_555 111.1 ? 10 O ? F HOH . ? A HOH 84 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 O ? F HOH . ? A HOH 85 ? 1_555 99.6 ? 11 OP2 ? A DA 8 ? A DA 8 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 OP1 ? B DG 4 ? B DG 14 ? 4_556 175.3 ? 12 O ? F HOH . ? A HOH 82 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 OP1 ? B DG 4 ? B DG 14 ? 4_556 104.1 ? 13 O ? F HOH . ? A HOH 83 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 OP1 ? B DG 4 ? B DG 14 ? 4_556 93.6 ? 14 O ? F HOH . ? A HOH 84 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 OP1 ? B DG 4 ? B DG 14 ? 4_556 99.4 ? 15 O ? F HOH . ? A HOH 85 ? 1_555 CA ? D CA . ? A CA 23 ? 1_555 OP1 ? B DG 4 ? B DG 14 ? 4_556 90.2 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A DIM 21 ? 12 'BINDING SITE FOR RESIDUE DIM A 21' AC2 Software B DIM 22 ? 9 'BINDING SITE FOR RESIDUE DIM B 22' AC3 Software A CA 23 ? 6 'BINDING SITE FOR RESIDUE CA A 23' 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 12 DC A 1 ? DC A 1 . ? 1_556 ? 2 AC1 12 DC A 7 ? DC A 7 . ? 1_555 ? 3 AC1 12 DC A 7 ? DC A 7 . ? 4_456 ? 4 AC1 12 DA A 8 ? DA A 8 . ? 1_555 ? 5 AC1 12 DT A 9 ? DT A 9 . ? 1_555 ? 6 AC1 12 DG A 10 ? DG A 10 . ? 1_555 ? 7 AC1 12 HOH F . ? HOH A 46 . ? 1_555 ? 8 AC1 12 HOH F . ? HOH A 75 . ? 1_555 ? 9 AC1 12 DA B 2 ? DA B 12 . ? 1_555 ? 10 AC1 12 DT B 3 ? DT B 13 . ? 1_555 ? 11 AC1 12 DG B 4 ? DG B 14 . ? 1_555 ? 12 AC1 12 DIM E . ? DIM B 22 . ? 1_555 ? 13 AC2 9 DG A 4 ? DG A 4 . ? 1_555 ? 14 AC2 9 DG A 5 ? DG A 5 . ? 1_555 ? 15 AC2 9 DIM C . ? DIM A 21 . ? 1_555 ? 16 AC2 9 HOH F . ? HOH A 46 . ? 1_555 ? 17 AC2 9 DG B 4 ? DG B 14 . ? 1_555 ? 18 AC2 9 DG B 5 ? DG B 15 . ? 1_555 ? 19 AC2 9 DC B 6 ? DC B 16 . ? 1_555 ? 20 AC2 9 DC B 7 ? DC B 17 . ? 1_555 ? 21 AC2 9 DA B 8 ? DA B 18 . ? 1_555 ? 22 AC3 6 DA A 8 ? DA A 8 . ? 1_555 ? 23 AC3 6 HOH F . ? HOH A 82 . ? 1_555 ? 24 AC3 6 HOH F . ? HOH A 83 . ? 1_555 ? 25 AC3 6 HOH F . ? HOH A 84 . ? 1_555 ? 26 AC3 6 HOH F . ? HOH A 85 . ? 1_555 ? 27 AC3 6 DG B 4 ? DG B 14 . ? 4_556 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? 1.493 1.420 0.073 0.011 N 2 1 "O4'" A DC 1 ? ? "C4'" A DC 1 ? ? 1.364 1.446 -0.082 0.010 N 3 1 P A DA 2 ? ? "O5'" A DA 2 ? ? 1.666 1.593 0.073 0.010 N 4 1 "O4'" A DT 3 ? ? "C4'" A DT 3 ? ? 1.343 1.446 -0.103 0.010 N 5 1 N3 A DT 3 ? ? C4 A DT 3 ? ? 1.331 1.382 -0.051 0.008 N 6 1 C5 A DT 3 ? ? C6 A DT 3 ? ? 1.268 1.339 -0.071 0.007 N 7 1 C6 A DT 3 ? ? N1 A DT 3 ? ? 1.331 1.378 -0.047 0.007 N 8 1 C4 A DT 3 ? ? O4 A DT 3 ? ? 1.294 1.228 0.066 0.009 N 9 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? 1.491 1.420 0.071 0.011 N 10 1 N1 A DG 5 ? ? C2 A DG 5 ? ? 1.320 1.373 -0.053 0.008 N 11 1 C2 A DG 5 ? ? N3 A DG 5 ? ? 1.377 1.323 0.054 0.008 N 12 1 "O4'" A DC 6 ? ? "C4'" A DC 6 ? ? 1.370 1.446 -0.076 0.010 N 13 1 N3 A DC 6 ? ? C4 A DC 6 ? ? 1.388 1.335 0.053 0.007 N 14 1 C2 A DC 7 ? ? N3 A DC 7 ? ? 1.403 1.353 0.050 0.008 N 15 1 N1 A DA 8 ? ? C2 A DA 8 ? ? 1.409 1.339 0.070 0.009 N 16 1 C6 A DA 8 ? ? N6 A DA 8 ? ? 1.278 1.335 -0.057 0.008 N 17 1 P A DT 9 ? ? "O5'" A DT 9 ? ? 1.697 1.593 0.104 0.010 N 18 1 C4 A DT 9 ? ? O4 A DT 9 ? ? 1.294 1.228 0.066 0.009 N 19 1 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? 1.492 1.420 0.072 0.011 N 20 1 "O4'" B DA 12 ? ? "C4'" B DA 12 ? ? 1.335 1.446 -0.111 0.010 N 21 1 P B DT 13 ? ? "O5'" B DT 13 ? ? 1.671 1.593 0.078 0.010 N 22 1 P B DG 14 ? ? "O5'" B DG 14 ? ? 1.509 1.593 -0.084 0.010 N 23 1 "C2'" B DG 14 ? ? "C1'" B DG 14 ? ? 1.446 1.518 -0.072 0.010 N 24 1 "O4'" B DG 14 ? ? "C4'" B DG 14 ? ? 1.377 1.446 -0.069 0.010 N 25 1 C2 B DG 14 ? ? N3 B DG 14 ? ? 1.373 1.323 0.050 0.008 N 26 1 N7 B DG 15 ? ? C8 B DG 15 ? ? 1.240 1.305 -0.065 0.006 N 27 1 "C5'" B DC 17 ? ? "C4'" B DC 17 ? ? 1.555 1.512 0.043 0.007 N 28 1 "O4'" B DC 17 ? ? "C1'" B DC 17 ? ? 1.486 1.420 0.066 0.011 N 29 1 C2 B DC 17 ? ? N3 B DC 17 ? ? 1.408 1.353 0.055 0.008 N 30 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? 1.508 1.420 0.088 0.011 N 31 1 N3 B DA 18 ? ? C4 B DA 18 ? ? 1.304 1.344 -0.040 0.006 N 32 1 "O4'" B DT 19 ? ? "C4'" B DT 19 ? ? 1.308 1.446 -0.138 0.010 N 33 1 C6 B DG 20 ? ? N1 B DG 20 ? ? 1.328 1.391 -0.063 0.007 N 34 1 N7 B DG 20 ? ? C8 B DG 20 ? ? 1.242 1.305 -0.063 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A DC 1 ? ? "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 104.27 109.40 -5.13 0.80 N 2 1 N1 A DC 1 ? ? C2 A DC 1 ? ? N3 A DC 1 ? ? 114.35 119.20 -4.85 0.70 N 3 1 C2 A DC 1 ? ? N3 A DC 1 ? ? C4 A DC 1 ? ? 125.39 119.90 5.49 0.50 N 4 1 C5 A DC 1 ? ? C6 A DC 1 ? ? N1 A DC 1 ? ? 124.86 121.00 3.86 0.50 N 5 1 N3 A DC 1 ? ? C4 A DC 1 ? ? N4 A DC 1 ? ? 122.84 118.00 4.84 0.70 N 6 1 OP1 A DA 2 ? ? P A DA 2 ? ? OP2 A DA 2 ? ? 135.06 119.60 15.46 1.50 N 7 1 "O5'" A DA 2 ? ? P A DA 2 ? ? OP2 A DA 2 ? ? 99.22 105.70 -6.48 0.90 N 8 1 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 100.93 108.00 -7.07 0.70 N 9 1 C6 A DA 2 ? ? N1 A DA 2 ? ? C2 A DA 2 ? ? 122.24 118.60 3.64 0.60 N 10 1 C5 A DA 2 ? ? C6 A DA 2 ? ? N1 A DA 2 ? ? 112.93 117.70 -4.77 0.50 N 11 1 N1 A DA 2 ? ? C6 A DA 2 ? ? N6 A DA 2 ? ? 124.66 118.60 6.06 0.60 N 12 1 C2 A DT 3 ? ? N3 A DT 3 ? ? C4 A DT 3 ? ? 120.22 127.20 -6.98 0.60 N 13 1 N3 A DT 3 ? ? C4 A DT 3 ? ? C5 A DT 3 ? ? 120.81 115.20 5.61 0.60 N 14 1 N3 A DT 3 ? ? C2 A DT 3 ? ? O2 A DT 3 ? ? 117.27 122.30 -5.03 0.60 N 15 1 N3 A DT 3 ? ? C4 A DT 3 ? ? O4 A DT 3 ? ? 110.63 119.90 -9.27 0.60 N 16 1 "C3'" A DT 3 ? ? "O3'" A DT 3 ? ? P A DG 4 ? ? 130.42 119.70 10.72 1.20 Y 17 1 "O5'" A DG 4 ? ? P A DG 4 ? ? OP1 A DG 4 ? ? 120.99 110.70 10.29 1.20 N 18 1 "C5'" A DG 4 ? ? "C4'" A DG 4 ? ? "O4'" A DG 4 ? ? 122.17 109.80 12.37 1.10 N 19 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 102.50 108.00 -5.50 0.70 N 20 1 C5 A DG 4 ? ? C6 A DG 4 ? ? O6 A DG 4 ? ? 124.01 128.60 -4.59 0.60 N 21 1 "O5'" A DG 5 ? ? "C5'" A DG 5 ? ? "C4'" A DG 5 ? ? 100.48 109.40 -8.92 0.80 N 22 1 "C3'" A DG 5 ? ? "C2'" A DG 5 ? ? "C1'" A DG 5 ? ? 94.49 102.40 -7.91 0.80 N 23 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 114.86 108.30 6.56 0.30 N 24 1 C2 A DG 5 ? ? N3 A DG 5 ? ? C4 A DG 5 ? ? 108.82 111.90 -3.08 0.50 N 25 1 "C3'" A DG 5 ? ? "O3'" A DG 5 ? ? P A DC 6 ? ? 129.27 119.70 9.57 1.20 Y 26 1 "O5'" A DC 6 ? ? P A DC 6 ? ? OP2 A DC 6 ? ? 118.74 110.70 8.04 1.20 N 27 1 "O5'" A DC 6 ? ? "C5'" A DC 6 ? ? "C4'" A DC 6 ? ? 101.40 109.40 -8.00 0.80 N 28 1 "O5'" A DC 7 ? ? "C5'" A DC 7 ? ? "C4'" A DC 7 ? ? 102.85 109.40 -6.55 0.80 N 29 1 N3 A DC 7 ? ? C4 A DC 7 ? ? N4 A DC 7 ? ? 126.45 118.00 8.45 0.70 N 30 1 C5 A DC 7 ? ? C4 A DC 7 ? ? N4 A DC 7 ? ? 113.23 120.20 -6.97 0.70 N 31 1 "C3'" A DC 7 ? ? "O3'" A DC 7 ? ? P A DA 8 ? ? 135.26 119.70 15.56 1.20 Y 32 1 "O5'" A DA 8 ? ? P A DA 8 ? ? OP2 A DA 8 ? ? 93.53 105.70 -12.17 0.90 N 33 1 "C5'" A DA 8 ? ? "C4'" A DA 8 ? ? "O4'" A DA 8 ? ? 117.31 109.80 7.51 1.10 N 34 1 C6 A DA 8 ? ? N1 A DA 8 ? ? C2 A DA 8 ? ? 123.01 118.60 4.41 0.60 N 35 1 N1 A DA 8 ? ? C2 A DA 8 ? ? N3 A DA 8 ? ? 124.47 129.30 -4.83 0.50 N 36 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N1 A DA 8 ? ? 114.66 117.70 -3.04 0.50 N 37 1 "O5'" A DT 9 ? ? P A DT 9 ? ? OP2 A DT 9 ? ? 100.07 105.70 -5.63 0.90 N 38 1 "O4'" A DT 9 ? ? "C4'" A DT 9 ? ? "C3'" A DT 9 ? ? 101.51 104.50 -2.99 0.40 N 39 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 110.64 108.30 2.34 0.30 N 40 1 C6 A DG 10 ? ? N1 A DG 10 ? ? C2 A DG 10 ? ? 121.24 125.10 -3.86 0.60 N 41 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 117.07 111.50 5.57 0.50 N 42 1 C5 A DG 10 ? ? C6 A DG 10 ? ? O6 A DG 10 ? ? 123.53 128.60 -5.07 0.60 N 43 1 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 97.95 102.20 -4.25 0.70 N 44 1 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 97.28 108.00 -10.72 0.70 N 45 1 C6 B DA 12 ? ? N1 B DA 12 ? ? C2 B DA 12 ? ? 122.39 118.60 3.79 0.60 N 46 1 C2 B DA 12 ? ? N3 B DA 12 ? ? C4 B DA 12 ? ? 107.24 110.60 -3.36 0.50 N 47 1 C5 B DA 12 ? ? C6 B DA 12 ? ? N1 B DA 12 ? ? 113.57 117.70 -4.13 0.50 N 48 1 N1 B DA 12 ? ? C6 B DA 12 ? ? N6 B DA 12 ? ? 123.66 118.60 5.06 0.60 N 49 1 C2 B DT 13 ? ? N3 B DT 13 ? ? C4 B DT 13 ? ? 122.05 127.20 -5.15 0.60 N 50 1 N3 B DT 13 ? ? C4 B DT 13 ? ? C5 B DT 13 ? ? 119.88 115.20 4.68 0.60 N 51 1 N3 B DT 13 ? ? C2 B DT 13 ? ? O2 B DT 13 ? ? 115.97 122.30 -6.33 0.60 N 52 1 N3 B DT 13 ? ? C4 B DT 13 ? ? O4 B DT 13 ? ? 113.65 119.90 -6.25 0.60 N 53 1 "C3'" B DT 13 ? ? "O3'" B DT 13 ? ? P B DG 14 ? ? 133.72 119.70 14.02 1.20 Y 54 1 "O3'" B DT 13 ? ? P B DG 14 ? ? OP1 B DG 14 ? ? 91.11 105.20 -14.09 2.20 Y 55 1 OP1 B DG 14 ? ? P B DG 14 ? ? OP2 B DG 14 ? ? 109.83 119.60 -9.77 1.50 N 56 1 "O5'" B DG 14 ? ? P B DG 14 ? ? OP2 B DG 14 ? ? 124.18 110.70 13.48 1.20 N 57 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 99.34 108.00 -8.66 0.70 N 58 1 C6 B DG 14 ? ? N1 B DG 14 ? ? C2 B DG 14 ? ? 119.13 125.10 -5.97 0.60 N 59 1 C5 B DG 14 ? ? C6 B DG 14 ? ? N1 B DG 14 ? ? 116.98 111.50 5.48 0.50 N 60 1 C5 B DG 14 ? ? C6 B DG 14 ? ? O6 B DG 14 ? ? 122.17 128.60 -6.43 0.60 N 61 1 "O4'" B DG 15 ? ? "C1'" B DG 15 ? ? N9 B DG 15 ? ? 101.31 108.00 -6.69 0.70 N 62 1 N3 B DG 15 ? ? C2 B DG 15 ? ? N2 B DG 15 ? ? 114.34 119.90 -5.56 0.70 N 63 1 N1 B DG 15 ? ? C6 B DG 15 ? ? O6 B DG 15 ? ? 124.01 119.90 4.11 0.60 N 64 1 C5 B DG 15 ? ? C6 B DG 15 ? ? O6 B DG 15 ? ? 122.92 128.60 -5.68 0.60 N 65 1 "C3'" B DG 15 ? ? "O3'" B DG 15 ? ? P B DC 16 ? ? 129.93 119.70 10.23 1.20 Y 66 1 C6 B DC 16 ? ? N1 B DC 16 ? ? C2 B DC 16 ? ? 123.45 120.30 3.15 0.40 N 67 1 P B DC 17 ? ? "O5'" B DC 17 ? ? "C5'" B DC 17 ? ? 133.24 120.90 12.34 1.60 N 68 1 "O4'" B DC 17 ? ? "C4'" B DC 17 ? ? "C3'" B DC 17 ? ? 102.07 104.50 -2.43 0.40 N 69 1 "C5'" B DC 17 ? ? "C4'" B DC 17 ? ? "O4'" B DC 17 ? ? 116.96 109.80 7.16 1.10 N 70 1 "C4'" B DC 17 ? ? "C3'" B DC 17 ? ? "C2'" B DC 17 ? ? 109.10 103.10 6.00 0.90 N 71 1 "C3'" B DC 17 ? ? "C2'" B DC 17 ? ? "C1'" B DC 17 ? ? 97.35 102.40 -5.05 0.80 N 72 1 C5 B DC 17 ? ? C6 B DC 17 ? ? N1 B DC 17 ? ? 126.89 121.00 5.89 0.50 N 73 1 C6 B DC 17 ? ? N1 B DC 17 ? ? "C1'" B DC 17 ? ? 130.17 120.80 9.37 1.20 N 74 1 C2 B DC 17 ? ? N1 B DC 17 ? ? "C1'" B DC 17 ? ? 110.66 118.80 -8.14 1.10 N 75 1 C6 B DA 18 ? ? N1 B DA 18 ? ? C2 B DA 18 ? ? 124.53 118.60 5.93 0.60 N 76 1 N1 B DA 18 ? ? C2 B DA 18 ? ? N3 B DA 18 ? ? 124.14 129.30 -5.16 0.50 N 77 1 C5 B DA 18 ? ? C6 B DA 18 ? ? N1 B DA 18 ? ? 112.73 117.70 -4.97 0.50 N 78 1 "C3'" B DA 18 ? ? "O3'" B DA 18 ? ? P B DT 19 ? ? 129.24 119.70 9.54 1.20 Y 79 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 103.32 108.00 -4.68 0.70 N 80 1 N1 B DT 19 ? ? C2 B DT 19 ? ? N3 B DT 19 ? ? 120.29 114.60 5.69 0.60 N 81 1 C2 B DT 19 ? ? N3 B DT 19 ? ? C4 B DT 19 ? ? 119.03 127.20 -8.17 0.60 N 82 1 N3 B DT 19 ? ? C4 B DT 19 ? ? C5 B DT 19 ? ? 120.01 115.20 4.81 0.60 N 83 1 N3 B DT 19 ? ? C2 B DT 19 ? ? O2 B DT 19 ? ? 118.66 122.30 -3.64 0.60 N 84 1 N3 B DT 19 ? ? C4 B DT 19 ? ? O4 B DT 19 ? ? 114.89 119.90 -5.01 0.60 N 85 1 C6 B DT 19 ? ? C5 B DT 19 ? ? C7 B DT 19 ? ? 117.94 122.90 -4.96 0.60 N 86 1 "O3'" B DT 19 ? ? P B DG 20 ? ? OP2 B DG 20 ? ? 120.95 110.50 10.45 1.10 Y 87 1 "O4'" B DG 20 ? ? "C1'" B DG 20 ? ? N9 B DG 20 ? ? 111.32 108.30 3.02 0.30 N 88 1 N3 B DG 20 ? ? C2 B DG 20 ? ? N2 B DG 20 ? ? 115.20 119.90 -4.70 0.70 N 89 1 N1 B DG 20 ? ? C6 B DG 20 ? ? O6 B DG 20 ? ? 126.07 119.90 6.17 0.60 N 90 1 C5 B DG 20 ? ? C6 B DG 20 ? ? O6 B DG 20 ? ? 119.63 128.60 -8.97 0.60 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal CA CA CA N N 1 DA OP3 O N N 2 DA P P N N 3 DA OP1 O N N 4 DA OP2 O N N 5 DA "O5'" O N N 6 DA "C5'" C N N 7 DA "C4'" C N R 8 DA "O4'" O N N 9 DA "C3'" C N S 10 DA "O3'" O N N 11 DA "C2'" C N N 12 DA "C1'" C N R 13 DA N9 N Y N 14 DA C8 C Y N 15 DA N7 N Y N 16 DA C5 C Y N 17 DA C6 C Y N 18 DA N6 N N N 19 DA N1 N Y N 20 DA C2 C Y N 21 DA N3 N Y N 22 DA C4 C Y N 23 DA HOP3 H N N 24 DA HOP2 H N N 25 DA "H5'" H N N 26 DA "H5''" H N N 27 DA "H4'" H N N 28 DA "H3'" H N N 29 DA "HO3'" H N N 30 DA "H2'" H N N 31 DA "H2''" H N N 32 DA "H1'" H N N 33 DA H8 H N N 34 DA H61 H N N 35 DA H62 H N N 36 DA H2 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 DIM O1 O N N 109 DIM C1 C N N 110 DIM N1 N N N 111 DIM C2 C Y N 112 DIM N2 N Y N 113 DIM C3 C Y N 114 DIM N3 N Y N 115 DIM C4 C Y N 116 DIM C5 C N N 117 DIM C6 C N N 118 DIM O2 O N N 119 DIM N4 N N N 120 DIM C7 C Y N 121 DIM N5 N Y N 122 DIM C8 C Y N 123 DIM N6 N Y N 124 DIM C9 C Y N 125 DIM C10 C N N 126 DIM C11 C N N 127 DIM O3 O N N 128 DIM N7 N N N 129 DIM C12 C N N 130 DIM C13 C N N 131 DIM C14 C N N 132 DIM N9 N N N 133 DIM N8 N N N 134 DIM H1 H N N 135 DIM HN1 H N N 136 DIM H4 H N N 137 DIM H51 H N N 138 DIM H52 H N N 139 DIM H53 H N N 140 DIM HN4 H N N 141 DIM H9 H N N 142 DIM H101 H N N 143 DIM H102 H N N 144 DIM H103 H N N 145 DIM HN7 H N N 146 DIM H121 H N N 147 DIM H122 H N N 148 DIM H131 H N N 149 DIM H132 H N N 150 DIM HN91 H N N 151 DIM HN92 H N N 152 DIM HN81 H N N 153 DIM HN82 H N N 154 DT OP3 O N N 155 DT P P N N 156 DT OP1 O N N 157 DT OP2 O N N 158 DT "O5'" O N N 159 DT "C5'" C N N 160 DT "C4'" C N R 161 DT "O4'" O N N 162 DT "C3'" C N S 163 DT "O3'" O N N 164 DT "C2'" C N N 165 DT "C1'" C N R 166 DT N1 N N N 167 DT C2 C N N 168 DT O2 O N N 169 DT N3 N N N 170 DT C4 C N N 171 DT O4 O N N 172 DT C5 C N N 173 DT C7 C N N 174 DT C6 C N N 175 DT HOP3 H N N 176 DT HOP2 H N N 177 DT "H5'" H N N 178 DT "H5''" H N N 179 DT "H4'" H N N 180 DT "H3'" H N N 181 DT "HO3'" H N N 182 DT "H2'" H N N 183 DT "H2''" H N N 184 DT "H1'" H N N 185 DT H3 H N N 186 DT H71 H N N 187 DT H72 H N N 188 DT H73 H N N 189 DT H6 H N N 190 HOH O O N N 191 HOH H1 H N N 192 HOH H2 H N N 193 # 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 DIM O1 C1 doub N N 113 DIM C1 N1 sing N N 114 DIM C1 H1 sing N N 115 DIM N1 C2 sing N N 116 DIM N1 HN1 sing N N 117 DIM C2 N2 sing Y N 118 DIM C2 C4 doub Y N 119 DIM N2 C3 doub Y N 120 DIM C3 N3 sing Y N 121 DIM C3 C6 sing N N 122 DIM N3 C4 sing Y N 123 DIM N3 C5 sing N N 124 DIM C4 H4 sing N N 125 DIM C5 H51 sing N N 126 DIM C5 H52 sing N N 127 DIM C5 H53 sing N N 128 DIM C6 O2 doub N N 129 DIM C6 N4 sing N N 130 DIM N4 C7 sing N N 131 DIM N4 HN4 sing N N 132 DIM C7 N5 sing Y N 133 DIM C7 C9 doub Y N 134 DIM N5 C8 doub Y N 135 DIM C8 N6 sing Y N 136 DIM C8 C11 sing N N 137 DIM N6 C9 sing Y N 138 DIM N6 C10 sing N N 139 DIM C9 H9 sing N N 140 DIM C10 H101 sing N N 141 DIM C10 H102 sing N N 142 DIM C10 H103 sing N N 143 DIM C11 O3 doub N N 144 DIM C11 N7 sing N N 145 DIM N7 C12 sing N N 146 DIM N7 HN7 sing N N 147 DIM C12 C13 sing N N 148 DIM C12 H121 sing N N 149 DIM C12 H122 sing N N 150 DIM C13 C14 sing N N 151 DIM C13 H131 sing N N 152 DIM C13 H132 sing N N 153 DIM C14 N9 doub N N 154 DIM C14 N8 sing N N 155 DIM N9 HN91 sing N N 156 DIM N9 HN92 sing N N 157 DIM N8 HN81 sing N N 158 DIM N8 HN82 sing N N 159 DT OP3 P sing N N 160 DT OP3 HOP3 sing N N 161 DT P OP1 doub N N 162 DT P OP2 sing N N 163 DT P "O5'" sing N N 164 DT OP2 HOP2 sing N N 165 DT "O5'" "C5'" sing N N 166 DT "C5'" "C4'" sing N N 167 DT "C5'" "H5'" sing N N 168 DT "C5'" "H5''" sing N N 169 DT "C4'" "O4'" sing N N 170 DT "C4'" "C3'" sing N N 171 DT "C4'" "H4'" sing N N 172 DT "O4'" "C1'" sing N N 173 DT "C3'" "O3'" sing N N 174 DT "C3'" "C2'" sing N N 175 DT "C3'" "H3'" sing N N 176 DT "O3'" "HO3'" sing N N 177 DT "C2'" "C1'" sing N N 178 DT "C2'" "H2'" sing N N 179 DT "C2'" "H2''" sing N N 180 DT "C1'" N1 sing N N 181 DT "C1'" "H1'" sing N N 182 DT N1 C2 sing N N 183 DT N1 C6 sing N N 184 DT C2 O2 doub N N 185 DT C2 N3 sing N N 186 DT N3 C4 sing N N 187 DT N3 H3 sing N N 188 DT C4 O4 doub N N 189 DT C4 C5 sing N N 190 DT C5 C7 sing N N 191 DT C5 C6 doub N N 192 DT C7 H71 sing N N 193 DT C7 H72 sing N N 194 DT C7 H73 sing N N 195 DT C6 H6 sing N N 196 HOH O H1 sing N N 197 HOH O H2 sing N N 198 # _ndb_struct_conf_na.entry_id 334D _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 0.276 -0.231 0.071 -8.809 -6.621 -3.594 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DA 2 1_555 B DT 9 1_555 -0.036 -0.133 0.141 -8.484 -9.885 1.265 2 A_DA2:DT19_B A 2 ? B 19 ? 20 1 1 A DT 3 1_555 B DA 8 1_555 -0.350 -0.040 -0.062 0.034 -8.610 -2.805 3 A_DT3:DA18_B A 3 ? B 18 ? 20 1 1 A DG 4 1_555 B DC 7 1_555 -0.445 -0.038 0.121 -2.142 -11.985 0.001 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 1 A DG 5 1_555 B DC 6 1_555 -0.173 -0.058 0.258 3.453 -18.606 1.078 5 A_DG5:DC16_B A 5 ? B 16 ? 19 1 1 A DC 6 1_555 B DG 5 1_555 0.440 -0.084 -0.077 -4.922 -19.579 -0.817 6 A_DC6:DG15_B A 6 ? B 15 ? 19 1 1 A DC 7 1_555 B DG 4 1_555 0.048 -0.267 0.076 -4.463 -5.974 -6.062 7 A_DC7:DG14_B A 7 ? B 14 ? 19 1 1 A DA 8 1_555 B DT 3 1_555 -0.067 -0.018 0.114 1.481 -9.831 -2.187 8 A_DA8:DT13_B A 8 ? B 13 ? 20 1 1 A DT 9 1_555 B DA 2 1_555 -0.068 -0.054 -0.068 1.661 -7.486 7.736 9 A_DT9:DA12_B A 9 ? B 12 ? 20 1 1 A DG 10 1_555 B DC 1 1_555 0.034 -0.169 -0.030 7.369 -7.962 -1.467 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 DA 2 1_555 B DT 9 1_555 -0.135 0.738 3.337 -2.140 7.567 32.170 -0.042 -0.141 3.419 13.406 3.791 33.093 1 AA_DC1DA2:DT19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DA 2 1_555 B DT 9 1_555 A DT 3 1_555 B DA 8 1_555 -0.301 -0.008 3.208 1.542 2.531 27.727 -0.607 0.985 3.174 5.262 -3.207 27.882 2 AA_DA2DT3:DA18DT19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DT 3 1_555 B DA 8 1_555 A DG 4 1_555 B DC 7 1_555 -0.011 2.615 3.474 -0.414 -8.852 50.027 3.671 -0.016 3.001 -10.374 0.485 50.756 3 AA_DT3DG4:DC17DA18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DG 4 1_555 B DC 7 1_555 A DG 5 1_555 B DC 6 1_555 0.617 0.588 3.246 -3.030 8.723 27.069 -0.814 -1.947 3.191 17.985 6.246 28.573 4 AA_DG4DG5:DC16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DG 5 1_555 B DC 6 1_555 A DC 6 1_555 B DG 5 1_555 -0.693 0.024 3.453 1.183 4.436 39.192 -0.515 1.174 3.414 6.586 -1.757 39.450 5 AA_DG5DC6:DG15DC16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DC 6 1_555 B DG 5 1_555 A DC 7 1_555 B DG 4 1_555 -0.168 0.460 3.433 1.848 9.507 28.732 -1.179 0.722 3.391 18.507 -3.596 30.288 6 AA_DC6DC7:DG14DG15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DC 7 1_555 B DG 4 1_555 A DA 8 1_555 B DT 3 1_555 0.346 2.580 3.216 -0.294 -6.238 47.172 3.668 -0.451 2.871 -7.755 0.365 47.560 7 AA_DC7DA8:DT13DG14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DA 8 1_555 B DT 3 1_555 A DT 9 1_555 B DA 2 1_555 0.842 -0.021 3.375 1.322 1.405 28.532 -0.372 -1.393 3.405 2.847 -2.678 28.595 8 AA_DA8DT9:DA12DT13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DT 9 1_555 B DA 2 1_555 A DG 10 1_555 B DC 1 1_555 0.094 0.238 3.285 -0.886 8.294 35.956 -0.762 -0.271 3.255 13.217 1.412 36.879 9 AA_DT9DG10:DC11DA12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'AN IDEAL HELIX RMS FIT TO BDJ057' # _atom_sites.entry_id 334D _atom_sites.fract_transf_matrix[1][1] 0.027282 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023451 _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] 0.028832 _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 CA N O P # loop_