data_298D # _entry.id 298D # _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 298D pdb_0000298d 10.2210/pdb298d/pdb RCSB GDL044 ? ? WWPDB D_1000177711 ? ? # 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 1996-12-17 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 5 'Structure model' 1 4 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 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 '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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_site 5 5 '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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 298D _pdbx_database_status.recvd_initial_deposition_date 1996-10-10 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Trent, J.O.' 1 'Clark, G.R.' 2 'Kumar, A.' 3 'Wilson, W.D.' 4 'Boykin, D.W.' 5 'Hall, J.E.' 6 'Tidwell, R.R.' 7 'Blagburn, B.L.' 8 'Neidle, S.' 9 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Targeting the minor groove of DNA: crystal structures of two complexes between furan derivatives of berenil and the DNA dodecamer d(CGCGAATTCGCG)2. ; J.Med.Chem. 39 4554 4562 1996 JMCMAR US 0022-2623 0151 ? 8917643 10.1021/jm9604484 1 ;A Crystallographic and Spectroscopic Study of the Complex Between d(CGCGAATTCGCG)2 and 2,5-Bis(4-guanylphenyl)furan, an Analogue of Berenil. Structural Origins of Enhanced DNA-binding Affinity ; Biochemistry 35 5655 5661 1996 BICHAW US 0006-2960 0033 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Trent, J.O.' 1 ? primary 'Clark, G.R.' 2 ? primary 'Kumar, A.' 3 ? primary 'Wilson, W.D.' 4 ? primary 'Boykin, D.W.' 5 ? primary 'Hall, J.E.' 6 ? primary 'Tidwell, R.R.' 7 ? primary 'Blagburn, B.L.' 8 ? primary 'Neidle, S.' 9 ? 1 'Laughton, C.A.' 10 ? 1 'Tanious, F.' 11 ? 1 'Nunn, C.M.' 12 ? 1 'Boykin, D.W.' 13 ? 1 'Wilson, W.D.' 14 ? 1 'Neidle, S.' 15 ? # 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 nat ;DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') ; 3663.392 2 ? ? ? ? 2 non-polymer syn '2,5-BIS{[4-(N-ISOPROPYL)DIAMINOMETHYL]PHENYL}FURAN' 392.537 1 ? ? ? ? 3 water nat water 18.015 81 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _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 '2,5-BIS{[4-(N-ISOPROPYL)DIAMINOMETHYL]PHENYL}FURAN' D18 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 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 D18 non-polymer . '2,5-BIS{[4-(N-ISOPROPYL)DIAMINOMETHYL]PHENYL}FURAN' 'FURAMIDINE DERIVATIVE' 'C24 H32 N4 O' 392.537 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 # 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 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DC 3 15 15 DC C B . n B 1 4 DG 4 16 16 DG G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 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 D18 1 25 25 D18 D18 B . D 3 HOH 1 27 27 HOH HOH A . D 3 HOH 2 28 28 HOH HOH A . D 3 HOH 3 29 29 HOH HOH A . D 3 HOH 4 30 30 HOH HOH A . D 3 HOH 5 31 31 HOH HOH A . D 3 HOH 6 35 35 HOH HOH A . D 3 HOH 7 39 39 HOH HOH A . D 3 HOH 8 42 42 HOH HOH A . D 3 HOH 9 48 48 HOH HOH A . D 3 HOH 10 49 49 HOH HOH A . D 3 HOH 11 51 51 HOH HOH A . D 3 HOH 12 53 53 HOH HOH A . D 3 HOH 13 55 55 HOH HOH A . D 3 HOH 14 59 59 HOH HOH A . D 3 HOH 15 60 60 HOH HOH A . D 3 HOH 16 62 62 HOH HOH A . D 3 HOH 17 63 63 HOH HOH A . D 3 HOH 18 64 64 HOH HOH A . D 3 HOH 19 69 69 HOH HOH A . D 3 HOH 20 73 73 HOH HOH A . D 3 HOH 21 76 76 HOH HOH A . D 3 HOH 22 78 78 HOH HOH A . D 3 HOH 23 79 79 HOH HOH A . D 3 HOH 24 81 81 HOH HOH A . D 3 HOH 25 82 82 HOH HOH A . D 3 HOH 26 85 85 HOH HOH A . D 3 HOH 27 86 86 HOH HOH A . D 3 HOH 28 88 88 HOH HOH A . D 3 HOH 29 89 89 HOH HOH A . D 3 HOH 30 93 93 HOH HOH A . D 3 HOH 31 95 95 HOH HOH A . D 3 HOH 32 100 100 HOH HOH A . D 3 HOH 33 104 104 HOH HOH A . D 3 HOH 34 105 105 HOH HOH A . D 3 HOH 35 106 106 HOH HOH A . E 3 HOH 1 26 26 HOH HOH B . E 3 HOH 2 32 32 HOH HOH B . E 3 HOH 3 33 33 HOH HOH B . E 3 HOH 4 34 34 HOH HOH B . E 3 HOH 5 36 36 HOH HOH B . E 3 HOH 6 37 37 HOH HOH B . E 3 HOH 7 38 38 HOH HOH B . E 3 HOH 8 40 40 HOH HOH B . E 3 HOH 9 41 41 HOH HOH B . E 3 HOH 10 43 43 HOH HOH B . E 3 HOH 11 44 44 HOH HOH B . E 3 HOH 12 45 45 HOH HOH B . E 3 HOH 13 46 46 HOH HOH B . E 3 HOH 14 47 47 HOH HOH B . E 3 HOH 15 50 50 HOH HOH B . E 3 HOH 16 52 52 HOH HOH B . E 3 HOH 17 54 54 HOH HOH B . E 3 HOH 18 56 56 HOH HOH B . E 3 HOH 19 57 57 HOH HOH B . E 3 HOH 20 58 58 HOH HOH B . E 3 HOH 21 61 61 HOH HOH B . E 3 HOH 22 65 65 HOH HOH B . E 3 HOH 23 66 66 HOH HOH B . E 3 HOH 24 67 67 HOH HOH B . E 3 HOH 25 68 68 HOH HOH B . E 3 HOH 26 70 70 HOH HOH B . E 3 HOH 27 71 71 HOH HOH B . E 3 HOH 28 72 72 HOH HOH B . E 3 HOH 29 74 74 HOH HOH B . E 3 HOH 30 75 75 HOH HOH B . E 3 HOH 31 77 77 HOH HOH B . E 3 HOH 32 80 80 HOH HOH B . E 3 HOH 33 83 83 HOH HOH B . E 3 HOH 34 84 84 HOH HOH B . E 3 HOH 35 87 87 HOH HOH B . E 3 HOH 36 90 90 HOH HOH B . E 3 HOH 37 91 91 HOH HOH B . E 3 HOH 38 92 92 HOH HOH B . E 3 HOH 39 94 94 HOH HOH B . E 3 HOH 40 96 96 HOH HOH B . E 3 HOH 41 97 97 HOH HOH B . E 3 HOH 42 98 98 HOH HOH B . E 3 HOH 43 99 99 HOH HOH B . E 3 HOH 44 101 101 HOH HOH B . E 3 HOH 45 102 102 HOH HOH B . E 3 HOH 46 103 103 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR refinement . ? 1 XENGEN 'data reduction' 'V. 1.3' ? 2 # _cell.entry_id 298D _cell.length_a 24.600 _cell.length_b 40.070 _cell.length_c 65.450 _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 298D _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 298D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.20 _exptl_crystal.density_percent_sol 44.13 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 286.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 286.00K' _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 MGCL2 ? ? ? 1 4 1 SPERMINE ? ? ? 1 5 1 'NA CACODYLATE' ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 287.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type XENTRONICS _diffrn_detector.pdbx_collection_date 1995-09-12 _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 GRAPHITE _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 ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 298D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 2.200 _reflns.number_obs 3146 _reflns.number_all ? _reflns.percent_possible_obs 87.600 _reflns.pdbx_Rmerge_I_obs 0.0730000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 298D _refine.ls_number_reflns_obs 2591 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _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 2.200 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1690000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1690000 _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 BDL001 _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 486 _refine_hist.pdbx_number_atoms_ligand 29 _refine_hist.number_atoms_solvent 81 _refine_hist.number_atoms_total 596 _refine_hist.d_res_high 2.200 _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 x_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 1.53 ? ? ? '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' ? # _database_PDB_matrix.entry_id 298D _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 298D _struct.title ;TARGETING THE MINOR GROOVE OF DNA: CRYSTAL STRUCTURES OF TWO COMPLEXES BETWEEN FURAN DERIVATIVES OF BERENIL AND THE DNA DODECAMER D(CGCGAATTCGCG)2 ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 298D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 298D _struct_ref.pdbx_db_accession 298D _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 298D A 1 ? 12 ? 298D 1 ? 12 ? 1 12 2 1 298D B 1 ? 12 ? 298D 13 ? 24 ? 13 24 # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog18 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 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 D18 25 ? 13 'BINDING SITE FOR RESIDUE D18 B 25' 'DRUG BINDING SITE' ? ? ? ? ? ? ? # 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 13 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 13 DT A 7 ? DT A 7 . ? 1_555 ? 3 AC1 13 DT A 8 ? DT A 8 . ? 1_555 ? 4 AC1 13 DC A 9 ? DC A 9 . ? 1_555 ? 5 AC1 13 DA B 5 ? DA B 17 . ? 1_555 ? 6 AC1 13 DA B 6 ? DA B 18 . ? 1_555 ? 7 AC1 13 DT B 7 ? DT B 19 . ? 1_555 ? 8 AC1 13 DT B 8 ? DT B 20 . ? 1_555 ? 9 AC1 13 DC B 9 ? DC B 21 . ? 1_555 ? 10 AC1 13 HOH E . ? HOH B 57 . ? 1_555 ? 11 AC1 13 HOH E . ? HOH B 71 . ? 1_555 ? 12 AC1 13 HOH E . ? HOH B 72 . ? 1_555 ? 13 AC1 13 HOH E . ? HOH B 99 . ? 1_555 ? # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 C7 ? B D18 25 ? PLANAR . 2 1 "C7'" ? B D18 25 ? PLANAR . # 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 DC A 11 ? ? 0.075 'SIDE CHAIN' 2 1 DC B 21 ? ? 0.064 'SIDE CHAIN' 3 1 DG B 22 ? ? 0.051 'SIDE CHAIN' # _struct_site_keywords.site_id 'DRUG BINDING SITE' _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 D18 C10 C N N 1 D18 C9 C N N 2 D18 C8 C N N 3 D18 N2 N N N 4 D18 C7 C N S 5 D18 N1 N N N 6 D18 C1 C Y N 7 D18 C2 C Y N 8 D18 C3 C Y N 9 D18 C4 C Y N 10 D18 C5 C Y N 11 D18 C6 C Y N 12 D18 CA C Y N 13 D18 CB C Y N 14 D18 "CB'" C Y N 15 D18 "CA'" C Y N 16 D18 O1 O Y N 17 D18 "C1'" C Y N 18 D18 "C2'" C Y N 19 D18 "C3'" C Y N 20 D18 "C4'" C Y N 21 D18 "C5'" C Y N 22 D18 "C6'" C Y N 23 D18 "C7'" C N R 24 D18 "N1'" N N N 25 D18 "N2'" N N N 26 D18 "C8'" C N N 27 D18 "C9'" C N N 28 D18 CAX C N N 29 D18 H101 H N N 30 D18 H102 H N N 31 D18 H103 H N N 32 D18 H91 H N N 33 D18 H92 H N N 34 D18 H93 H N N 35 D18 H8 H N N 36 D18 HN2 H N N 37 D18 H7 H N N 38 D18 HN11 H N N 39 D18 HN12 H N N 40 D18 H2 H N N 41 D18 H3 H N N 42 D18 H5 H N N 43 D18 H6 H N N 44 D18 HB H N N 45 D18 "HB'" H N N 46 D18 "H2'" H N N 47 D18 "H3'" H N N 48 D18 "H5'" H N N 49 D18 "H6'" H N N 50 D18 "H7'" H N N 51 D18 "HN'1" H N N 52 D18 "HN'2" H N N 53 D18 "HN2'" H N N 54 D18 "H8'" H N N 55 D18 "H9'1" H N N 56 D18 "H9'2" H N N 57 D18 "H9'3" H N N 58 D18 "H1'1" H N N 59 D18 "H1'2" H N N 60 D18 "H1'3" H N N 61 DA OP3 O N N 62 DA P P N N 63 DA OP1 O N N 64 DA OP2 O N N 65 DA "O5'" O N N 66 DA "C5'" C N N 67 DA "C4'" C N R 68 DA "O4'" O N N 69 DA "C3'" C N S 70 DA "O3'" O N N 71 DA "C2'" C N N 72 DA "C1'" C N R 73 DA N9 N Y N 74 DA C8 C Y N 75 DA N7 N Y N 76 DA C5 C Y N 77 DA C6 C Y N 78 DA N6 N N N 79 DA N1 N Y N 80 DA C2 C Y N 81 DA N3 N Y N 82 DA C4 C Y N 83 DA HOP3 H N N 84 DA HOP2 H N N 85 DA "H5'" H N N 86 DA "H5''" H N N 87 DA "H4'" H N N 88 DA "H3'" H N N 89 DA "HO3'" H N N 90 DA "H2'" H N N 91 DA "H2''" H N N 92 DA "H1'" H N N 93 DA H8 H N N 94 DA H61 H N N 95 DA H62 H N N 96 DA H2 H N N 97 DC OP3 O N N 98 DC P P N N 99 DC OP1 O N N 100 DC OP2 O N N 101 DC "O5'" O N N 102 DC "C5'" C N N 103 DC "C4'" C N R 104 DC "O4'" O N N 105 DC "C3'" C N S 106 DC "O3'" O N N 107 DC "C2'" C N N 108 DC "C1'" C N R 109 DC N1 N N N 110 DC C2 C N N 111 DC O2 O N N 112 DC N3 N N N 113 DC C4 C N N 114 DC N4 N N N 115 DC C5 C N N 116 DC C6 C N N 117 DC HOP3 H N N 118 DC HOP2 H N N 119 DC "H5'" H N N 120 DC "H5''" H N N 121 DC "H4'" H N N 122 DC "H3'" H N N 123 DC "HO3'" H N N 124 DC "H2'" H N N 125 DC "H2''" H N N 126 DC "H1'" H N N 127 DC H41 H N N 128 DC H42 H N N 129 DC H5 H N N 130 DC H6 H N N 131 DG OP3 O N N 132 DG P P N N 133 DG OP1 O N N 134 DG OP2 O N N 135 DG "O5'" O N N 136 DG "C5'" C N N 137 DG "C4'" C N R 138 DG "O4'" O N N 139 DG "C3'" C N S 140 DG "O3'" O N N 141 DG "C2'" C N N 142 DG "C1'" C N R 143 DG N9 N Y N 144 DG C8 C Y N 145 DG N7 N Y N 146 DG C5 C Y N 147 DG C6 C N N 148 DG O6 O N N 149 DG N1 N N N 150 DG C2 C N N 151 DG N2 N N N 152 DG N3 N N N 153 DG C4 C Y N 154 DG HOP3 H N N 155 DG HOP2 H N N 156 DG "H5'" H N N 157 DG "H5''" H N N 158 DG "H4'" H N N 159 DG "H3'" H N N 160 DG "HO3'" H N N 161 DG "H2'" H N N 162 DG "H2''" H N N 163 DG "H1'" H N N 164 DG H8 H N N 165 DG H1 H N N 166 DG H21 H N N 167 DG H22 H N N 168 DT OP3 O N N 169 DT P P N N 170 DT OP1 O N N 171 DT OP2 O N N 172 DT "O5'" O N N 173 DT "C5'" C N N 174 DT "C4'" C N R 175 DT "O4'" O N N 176 DT "C3'" C N S 177 DT "O3'" O N N 178 DT "C2'" C N N 179 DT "C1'" C N R 180 DT N1 N N N 181 DT C2 C N N 182 DT O2 O N N 183 DT N3 N N N 184 DT C4 C N N 185 DT O4 O N N 186 DT C5 C N N 187 DT C7 C N N 188 DT C6 C N N 189 DT HOP3 H N N 190 DT HOP2 H N N 191 DT "H5'" H N N 192 DT "H5''" H N N 193 DT "H4'" H N N 194 DT "H3'" H N N 195 DT "HO3'" H N N 196 DT "H2'" H N N 197 DT "H2''" H N N 198 DT "H1'" H N N 199 DT H3 H N N 200 DT H71 H N N 201 DT H72 H N N 202 DT H73 H N N 203 DT H6 H N N 204 HOH O O N N 205 HOH H1 H N N 206 HOH H2 H N N 207 # 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 D18 C10 C8 sing N N 1 D18 C10 H101 sing N N 2 D18 C10 H102 sing N N 3 D18 C10 H103 sing N N 4 D18 C9 C8 sing N N 5 D18 C9 H91 sing N N 6 D18 C9 H92 sing N N 7 D18 C9 H93 sing N N 8 D18 C8 N2 sing N N 9 D18 C8 H8 sing N N 10 D18 N2 C7 sing N N 11 D18 N2 HN2 sing N N 12 D18 C7 N1 sing N N 13 D18 C7 C4 sing N N 14 D18 C7 H7 sing N N 15 D18 N1 HN11 sing N N 16 D18 N1 HN12 sing N N 17 D18 C1 C2 sing Y N 18 D18 C1 C6 doub Y N 19 D18 C1 CA sing Y N 20 D18 C2 C3 doub Y N 21 D18 C2 H2 sing N N 22 D18 C3 C4 sing Y N 23 D18 C3 H3 sing N N 24 D18 C4 C5 doub Y N 25 D18 C5 C6 sing Y N 26 D18 C5 H5 sing N N 27 D18 C6 H6 sing N N 28 D18 CA CB doub Y N 29 D18 CA O1 sing Y N 30 D18 CB "CB'" sing Y N 31 D18 CB HB sing N N 32 D18 "CB'" "CA'" doub Y N 33 D18 "CB'" "HB'" sing N N 34 D18 "CA'" O1 sing Y N 35 D18 "CA'" "C1'" sing Y N 36 D18 "C1'" "C2'" sing Y N 37 D18 "C1'" "C6'" doub Y N 38 D18 "C2'" "C3'" doub Y N 39 D18 "C2'" "H2'" sing N N 40 D18 "C3'" "C4'" sing Y N 41 D18 "C3'" "H3'" sing N N 42 D18 "C4'" "C5'" doub Y N 43 D18 "C4'" "C7'" sing N N 44 D18 "C5'" "C6'" sing Y N 45 D18 "C5'" "H5'" sing N N 46 D18 "C6'" "H6'" sing N N 47 D18 "C7'" "N1'" sing N N 48 D18 "C7'" "N2'" sing N N 49 D18 "C7'" "H7'" sing N N 50 D18 "N1'" "HN'1" sing N N 51 D18 "N1'" "HN'2" sing N N 52 D18 "N2'" "C8'" sing N N 53 D18 "N2'" "HN2'" sing N N 54 D18 "C8'" "C9'" sing N N 55 D18 "C8'" CAX sing N N 56 D18 "C8'" "H8'" sing N N 57 D18 "C9'" "H9'1" sing N N 58 D18 "C9'" "H9'2" sing N N 59 D18 "C9'" "H9'3" sing N N 60 D18 CAX "H1'1" sing N N 61 D18 CAX "H1'2" sing N N 62 D18 CAX "H1'3" sing N N 63 DA OP3 P sing N N 64 DA OP3 HOP3 sing N N 65 DA P OP1 doub N N 66 DA P OP2 sing N N 67 DA P "O5'" sing N N 68 DA OP2 HOP2 sing N N 69 DA "O5'" "C5'" sing N N 70 DA "C5'" "C4'" sing N N 71 DA "C5'" "H5'" sing N N 72 DA "C5'" "H5''" sing N N 73 DA "C4'" "O4'" sing N N 74 DA "C4'" "C3'" sing N N 75 DA "C4'" "H4'" sing N N 76 DA "O4'" "C1'" sing N N 77 DA "C3'" "O3'" sing N N 78 DA "C3'" "C2'" sing N N 79 DA "C3'" "H3'" sing N N 80 DA "O3'" "HO3'" sing N N 81 DA "C2'" "C1'" sing N N 82 DA "C2'" "H2'" sing N N 83 DA "C2'" "H2''" sing N N 84 DA "C1'" N9 sing N N 85 DA "C1'" "H1'" sing N N 86 DA N9 C8 sing Y N 87 DA N9 C4 sing Y N 88 DA C8 N7 doub Y N 89 DA C8 H8 sing N N 90 DA N7 C5 sing Y N 91 DA C5 C6 sing Y N 92 DA C5 C4 doub Y N 93 DA C6 N6 sing N N 94 DA C6 N1 doub Y N 95 DA N6 H61 sing N N 96 DA N6 H62 sing N N 97 DA N1 C2 sing Y N 98 DA C2 N3 doub Y N 99 DA C2 H2 sing N N 100 DA N3 C4 sing Y N 101 DC OP3 P sing N N 102 DC OP3 HOP3 sing N N 103 DC P OP1 doub N N 104 DC P OP2 sing N N 105 DC P "O5'" sing N N 106 DC OP2 HOP2 sing N N 107 DC "O5'" "C5'" sing N N 108 DC "C5'" "C4'" sing N N 109 DC "C5'" "H5'" sing N N 110 DC "C5'" "H5''" sing N N 111 DC "C4'" "O4'" sing N N 112 DC "C4'" "C3'" sing N N 113 DC "C4'" "H4'" sing N N 114 DC "O4'" "C1'" sing N N 115 DC "C3'" "O3'" sing N N 116 DC "C3'" "C2'" sing N N 117 DC "C3'" "H3'" sing N N 118 DC "O3'" "HO3'" sing N N 119 DC "C2'" "C1'" sing N N 120 DC "C2'" "H2'" sing N N 121 DC "C2'" "H2''" sing N N 122 DC "C1'" N1 sing N N 123 DC "C1'" "H1'" sing N N 124 DC N1 C2 sing N N 125 DC N1 C6 sing N N 126 DC C2 O2 doub N N 127 DC C2 N3 sing N N 128 DC N3 C4 doub N N 129 DC C4 N4 sing N N 130 DC C4 C5 sing N N 131 DC N4 H41 sing N N 132 DC N4 H42 sing N N 133 DC C5 C6 doub N N 134 DC C5 H5 sing N N 135 DC C6 H6 sing N N 136 DG OP3 P sing N N 137 DG OP3 HOP3 sing N N 138 DG P OP1 doub N N 139 DG P OP2 sing N N 140 DG P "O5'" sing N N 141 DG OP2 HOP2 sing N N 142 DG "O5'" "C5'" sing N N 143 DG "C5'" "C4'" sing N N 144 DG "C5'" "H5'" sing N N 145 DG "C5'" "H5''" sing N N 146 DG "C4'" "O4'" sing N N 147 DG "C4'" "C3'" sing N N 148 DG "C4'" "H4'" sing N N 149 DG "O4'" "C1'" sing N N 150 DG "C3'" "O3'" sing N N 151 DG "C3'" "C2'" sing N N 152 DG "C3'" "H3'" sing N N 153 DG "O3'" "HO3'" sing N N 154 DG "C2'" "C1'" sing N N 155 DG "C2'" "H2'" sing N N 156 DG "C2'" "H2''" sing N N 157 DG "C1'" N9 sing N N 158 DG "C1'" "H1'" sing N N 159 DG N9 C8 sing Y N 160 DG N9 C4 sing Y N 161 DG C8 N7 doub Y N 162 DG C8 H8 sing N N 163 DG N7 C5 sing Y N 164 DG C5 C6 sing N N 165 DG C5 C4 doub Y N 166 DG C6 O6 doub N N 167 DG C6 N1 sing N N 168 DG N1 C2 sing N N 169 DG N1 H1 sing N N 170 DG C2 N2 sing N N 171 DG C2 N3 doub N N 172 DG N2 H21 sing N N 173 DG N2 H22 sing N N 174 DG N3 C4 sing N N 175 DT OP3 P sing N N 176 DT OP3 HOP3 sing N N 177 DT P OP1 doub N N 178 DT P OP2 sing N N 179 DT P "O5'" sing N N 180 DT OP2 HOP2 sing N N 181 DT "O5'" "C5'" sing N N 182 DT "C5'" "C4'" sing N N 183 DT "C5'" "H5'" sing N N 184 DT "C5'" "H5''" sing N N 185 DT "C4'" "O4'" sing N N 186 DT "C4'" "C3'" sing N N 187 DT "C4'" "H4'" sing N N 188 DT "O4'" "C1'" sing N N 189 DT "C3'" "O3'" sing N N 190 DT "C3'" "C2'" sing N N 191 DT "C3'" "H3'" sing N N 192 DT "O3'" "HO3'" sing N N 193 DT "C2'" "C1'" sing N N 194 DT "C2'" "H2'" sing N N 195 DT "C2'" "H2''" sing N N 196 DT "C1'" N1 sing N N 197 DT "C1'" "H1'" sing N N 198 DT N1 C2 sing N N 199 DT N1 C6 sing N N 200 DT C2 O2 doub N N 201 DT C2 N3 sing N N 202 DT N3 C4 sing N N 203 DT N3 H3 sing N N 204 DT C4 O4 doub N N 205 DT C4 C5 sing N N 206 DT C5 C7 sing N N 207 DT C5 C6 doub N N 208 DT C7 H71 sing N N 209 DT C7 H72 sing N N 210 DT C7 H73 sing N N 211 DT C6 H6 sing N N 212 HOH O H1 sing N N 213 HOH O H2 sing N N 214 # _ndb_struct_conf_na.entry_id 298D _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 12 1_555 0.245 -0.240 -0.221 -0.229 -12.173 0.541 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.016 -0.319 -0.091 -1.907 -10.959 -1.341 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 -0.589 -0.157 0.058 -7.411 -5.881 -1.230 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.422 -0.343 -0.018 6.688 -9.352 -2.655 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.662 -0.227 0.035 -0.254 -16.742 0.763 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.238 -0.003 0.159 7.171 -21.590 8.465 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.015 0.284 0.241 2.405 -23.380 9.811 7 A_DT7:DA18_B A 7 ? B 18 ? ? ? 1 A DT 8 1_555 B DA 5 1_555 -0.327 -0.130 0.169 6.587 -15.221 0.881 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 -0.309 -0.314 -0.061 -5.365 -8.278 -3.000 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 0.081 -0.026 0.056 8.847 -5.652 7.694 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.083 -0.305 0.297 7.979 -19.473 2.321 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.377 -0.585 0.182 6.177 12.543 -7.232 12 A_DG12:DC13_B A 12 ? B 13 ? 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 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.310 0.342 3.466 -0.424 10.588 34.712 -1.050 0.435 3.424 17.256 0.691 36.246 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.487 0.421 3.399 2.082 -3.094 34.483 1.200 -0.485 3.372 -5.199 -3.500 34.678 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.206 0.489 3.102 -1.198 6.336 30.593 -0.252 0.164 3.143 11.843 2.239 31.249 3 AA_DC3DG4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 0.196 0.190 3.557 0.345 1.686 40.918 0.071 -0.239 3.563 2.411 -0.493 40.953 4 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.240 -0.431 3.006 -0.251 6.509 34.344 -1.611 -0.434 2.877 10.902 0.420 34.938 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.079 -0.422 3.460 -0.757 -2.582 33.503 -0.281 -0.269 3.479 -4.469 1.311 33.608 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.536 -0.239 3.114 0.809 1.413 32.832 -0.652 1.078 3.087 2.498 -1.431 32.871 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 0.006 0.078 3.603 2.391 1.155 38.047 -0.041 0.324 3.598 1.770 -3.662 38.136 8 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.615 1.345 3.216 1.517 -1.308 36.332 2.332 -0.778 3.189 -2.095 -2.430 36.385 9 AA_DC9DG10:DC15DG16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -0.871 0.710 3.417 -3.142 -5.221 38.437 1.726 0.910 3.354 -7.869 4.736 38.899 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 0.279 0.637 3.631 -1.077 -4.288 35.473 1.717 -0.626 3.523 -7.004 1.759 35.738 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_initial_refinement_model.accession_code 1BNA _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details BDL001 # _atom_sites.entry_id 298D _atom_sites.fract_transf_matrix[1][1] 0.040650 _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] 0.024956 _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] 0.015279 _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_