data_380D # _entry.id 380D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 380D pdb_0000380d 10.2210/pdb380d/pdb RCSB DDFB76 ? ? WWPDB D_1000178848 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 1998-07-13 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-11-26 5 'Structure model' 1 4 2024-02-21 # _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' Other 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 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 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' software 5 5 'Structure model' struct_conn 6 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_software.name' 4 5 'Structure model' '_struct_conn.pdbx_dist_value' 5 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 7 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 20 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 21 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 22 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 380D _pdbx_database_status.recvd_initial_deposition_date 1998-02-18 _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Dutta, R.' 1 'Gao, Y.-G.' 2 'Priebe, W.' 3 'Wang, A.H.-J.' 4 # _citation.id primary _citation.title ;Binding of the modified daunorubicin WP401 adjacent to a T-G base pair induces the reverse Watson-Crick conformation: crystal structures of the WP401-TGGCCG and WP401-CGG[br5C]CG complexes. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 26 _citation.page_first 3001 _citation.page_last 3005 _citation.year 1998 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9611247 _citation.pdbx_database_id_DOI 10.1093/nar/26.12.3001 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dutta, R.' 1 ? primary 'Gao, Y.G.' 2 ? primary 'Priebe, W.' 3 ? primary 'Wang, A.H.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man ;DNA (5'-D(*CP*GP*(G49)P*(CBR)P*CP*G)-3') ; 1903.128 2 ? ? ? ? 2 non-polymer syn "2'-BROMO-4'-EPIDAUNORUBICIN" 606.416 2 ? ? ? ? 3 water nat water 18.015 34 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(G49)(CBR)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGGCCG _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'-BROMO-4'-EPIDAUNORUBICIN" DM8 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 G49 n 1 4 CBR n 1 5 DC n 1 6 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 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 DM8 non-polymer . "2'-BROMO-4'-EPIDAUNORUBICIN" 'WP401; DAUNOMYCIN DERIVATIVE; DAUNORUBICIN DERIVATIVE' 'C27 H28 Br N O10' 606.416 G49 'DNA linking' n "N2-METHYL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O7 P' 361.248 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 G49 3 3 3 G49 +G A . n A 1 4 CBR 4 4 4 CBR BR A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n B 1 1 DC 1 7 7 DC C B . n B 1 2 DG 2 8 8 DG G B . n B 1 3 G49 3 9 9 G49 +G B . n B 1 4 CBR 4 10 10 CBR BR B . n B 1 5 DC 5 11 11 DC C B . n B 1 6 DG 6 12 12 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 DM8 1 7 3 DM8 DM8 A . D 2 DM8 1 13 9 DM8 DM8 B . E 3 HOH 1 18 18 HOH HOH A . E 3 HOH 2 19 19 HOH HOH A . E 3 HOH 3 22 22 HOH HOH A . E 3 HOH 4 24 24 HOH HOH A . E 3 HOH 5 26 26 HOH HOH A . E 3 HOH 6 30 30 HOH HOH A . E 3 HOH 7 31 31 HOH HOH A . E 3 HOH 8 33 33 HOH HOH A . E 3 HOH 9 35 35 HOH HOH A . E 3 HOH 10 40 40 HOH HOH A . E 3 HOH 11 41 41 HOH HOH A . E 3 HOH 12 44 44 HOH HOH A . E 3 HOH 13 45 45 HOH HOH A . E 3 HOH 14 47 47 HOH HOH A . F 3 HOH 1 15 15 HOH HOH B . F 3 HOH 2 16 16 HOH HOH B . F 3 HOH 3 17 17 HOH HOH B . F 3 HOH 4 20 20 HOH HOH B . F 3 HOH 5 21 21 HOH HOH B . F 3 HOH 6 23 23 HOH HOH B . F 3 HOH 7 25 25 HOH HOH B . F 3 HOH 8 27 27 HOH HOH B . F 3 HOH 9 28 28 HOH HOH B . F 3 HOH 10 29 29 HOH HOH B . F 3 HOH 11 32 32 HOH HOH B . F 3 HOH 12 34 34 HOH HOH B . F 3 HOH 13 36 36 HOH HOH B . F 3 HOH 14 37 37 HOH HOH B . F 3 HOH 15 38 38 HOH HOH B . F 3 HOH 16 39 39 HOH HOH B . F 3 HOH 17 42 42 HOH HOH B . F 3 HOH 18 43 43 HOH HOH B . F 3 HOH 19 46 46 HOH HOH B . F 3 HOH 20 48 48 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR refinement . ? 1 bioteX 'data reduction' 'V. 1.1' ? 2 bioteX 'data scaling' 'V. 1.1' ? 3 # _cell.entry_id 380D _cell.length_a 37.230 _cell.length_b 37.230 _cell.length_c 61.960 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 380D _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # _exptl.entry_id 380D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.82 _exptl_crystal.density_percent_sol 56.39 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 298.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.00 _exptl_crystal_grow.pdbx_details 'pH 6.00, VAPOR DIFFUSION, temperature 298.00K' _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 BACL2 ? ? ? 1 3 1 'SODIUM CACODYLATE' ? ? ? 1 4 1 SPERMINE ? ? ? 1 5 1 MPD ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 293.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type RIGAKU _diffrn_detector.pdbx_collection_date 1997-07-22 _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 . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source ? _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 380D _reflns.observed_criterion_sigma_I 1.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 10.000 _reflns.d_resolution_high 2.000 _reflns.number_obs 3416 _reflns.number_all ? _reflns.percent_possible_obs 94.500 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.50 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 380D _refine.ls_number_reflns_obs 3077 _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 10.000 _refine.ls_d_res_high 2.000 _refine.ls_percent_reflns_obs 85.310 _refine.ls_R_factor_obs 0.189 _refine.ls_R_factor_all 0.193 _refine.ls_R_factor_R_work 0.189 _refine.ls_R_factor_R_free 0.242 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.000 _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 ? _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.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _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.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 244 _refine_hist.pdbx_number_atoms_ligand 78 _refine_hist.number_atoms_solvent 34 _refine_hist.number_atoms_total 356 _refine_hist.d_res_high 2.000 _refine_hist.d_res_low 10.000 # 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 0.006 ? ? ? '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 0.91 ? ? ? '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 380D _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 380D _struct.title ;BINDING OF THE MODIFIED DAUNORUBICIN WP401 ADJACENT TO A T-G BASE PAIR INDUCES THE REVERSE WATSON-CRICK CONFORMATION: CRYSTAL STRUCTURES OF THE WP401-TGGCCG AND WP401-CGG[BR5C]CG COMPLEXES ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 380D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'RIGHT HANDED DNA, DOUBLE HELIX, MODIFIED, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 380D _struct_ref.pdbx_db_accession 380D _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 380D A 1 ? 6 ? 380D 1 ? 6 ? 1 6 2 1 380D B 1 ? 6 ? 380D 7 ? 12 ? 7 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 2 "O3'" ? ? ? 1_555 A G49 3 P ? ? A DG 2 A G49 3 1_555 ? ? ? ? ? ? ? 1.592 ? ? covale2 covale one ? A G49 3 "O3'" ? ? ? 1_555 A CBR 4 P ? ? A G49 3 A CBR 4 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale3 covale none ? A G49 3 CM2 ? ? ? 1_555 C DM8 . "N3'" ? ? A G49 3 A DM8 7 1_555 ? ? ? ? ? ? ? 1.432 ? ? covale4 covale both ? A CBR 4 "O3'" ? ? ? 1_555 A DC 5 P ? ? A CBR 4 A DC 5 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale5 covale both ? B DG 2 "O3'" ? ? ? 1_555 B G49 3 P ? ? B DG 8 B G49 9 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale6 covale one ? B G49 3 "O3'" ? ? ? 1_555 B CBR 4 P ? ? B G49 9 B CBR 10 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale7 covale none ? B G49 3 CM2 ? ? ? 1_555 D DM8 . "N3'" ? ? B G49 9 B DM8 13 1_555 ? ? ? ? ? ? ? 1.422 ? ? covale8 covale both ? B CBR 4 "O3'" ? ? ? 1_555 B DC 5 P ? ? B CBR 10 B DC 11 1_555 ? ? ? ? ? ? ? 1.598 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G49 3 N1 ? ? ? 1_555 B CBR 4 N3 ? ? A G49 3 B CBR 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G49 3 N2 ? ? ? 1_555 B CBR 4 O2 ? ? A G49 3 B CBR 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G49 3 O6 ? ? ? 1_555 B CBR 4 N4 ? ? A G49 3 B CBR 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A CBR 4 N3 ? ? ? 1_555 B G49 3 N1 ? ? A CBR 4 B G49 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A CBR 4 N4 ? ? ? 1_555 B G49 3 O6 ? ? A CBR 4 B G49 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A CBR 4 O2 ? ? ? 1_555 B G49 3 N2 ? ? A CBR 4 B G49 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 DM8 7 ? 12 'BINDING SITE FOR RESIDUE DM8 A 7' AC2 Software B DM8 13 ? 7 'BINDING SITE FOR RESIDUE DM8 B 13' 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_555 ? 2 AC1 12 DC A 1 ? DC A 1 . ? 3_554 ? 3 AC1 12 DG A 2 ? DG A 2 . ? 1_555 ? 4 AC1 12 G49 A 3 ? G49 A 3 . ? 1_555 ? 5 AC1 12 CBR A 4 ? CBR A 4 . ? 1_555 ? 6 AC1 12 DG A 6 ? DG A 6 . ? 6_455 ? 7 AC1 12 HOH E . ? HOH A 18 . ? 1_555 ? 8 AC1 12 DC B 5 ? DC B 11 . ? 1_555 ? 9 AC1 12 DG B 6 ? DG B 12 . ? 4_455 ? 10 AC1 12 DG B 6 ? DG B 12 . ? 1_555 ? 11 AC1 12 HOH F . ? HOH B 23 . ? 1_555 ? 12 AC1 12 HOH F . ? HOH B 36 . ? 4_455 ? 13 AC2 7 DC A 5 ? DC A 5 . ? 1_555 ? 14 AC2 7 DG A 6 ? DG A 6 . ? 1_555 ? 15 AC2 7 DC B 1 ? DC B 7 . ? 1_555 ? 16 AC2 7 DG B 2 ? DG B 8 . ? 1_555 ? 17 AC2 7 G49 B 3 ? G49 B 9 . ? 1_555 ? 18 AC2 7 CBR B 4 ? CBR B 10 . ? 1_555 ? 19 AC2 7 HOH F . ? HOH B 46 . ? 1_555 ? # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DC _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 11 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.096 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A G49 3 A G49 3 ? DG ? 2 A CBR 4 A CBR 4 ? DC ? 3 B G49 3 B G49 9 ? DG ? 4 B CBR 4 B CBR 10 ? DC ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text INTERCALATION # 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 CBR BR BR N N 1 CBR P P N N 2 CBR OP1 O N N 3 CBR OP2 O N N 4 CBR "O5'" O N N 5 CBR N1 N N N 6 CBR C6 C N N 7 CBR C2 C N N 8 CBR O2 O N N 9 CBR N3 N N N 10 CBR C4 C N N 11 CBR N4 N N N 12 CBR C5 C N N 13 CBR "C2'" C N N 14 CBR "C5'" C N N 15 CBR "C4'" C N R 16 CBR "O4'" O N N 17 CBR "C1'" C N R 18 CBR "C3'" C N S 19 CBR "O3'" O N N 20 CBR OP3 O N N 21 CBR HOP2 H N N 22 CBR H6 H N N 23 CBR H41 H N N 24 CBR H42 H N N 25 CBR "H2'" H N N 26 CBR "H2''" H N N 27 CBR "H5'" H N N 28 CBR "H5''" H N N 29 CBR "H4'" H N N 30 CBR "H1'" H N N 31 CBR "H3'" H N N 32 CBR "HO3'" H N N 33 CBR HOP3 H N N 34 DC OP3 O N N 35 DC P P N N 36 DC OP1 O N N 37 DC OP2 O N N 38 DC "O5'" O N N 39 DC "C5'" C N N 40 DC "C4'" C N R 41 DC "O4'" O N N 42 DC "C3'" C N S 43 DC "O3'" O N N 44 DC "C2'" C N N 45 DC "C1'" C N R 46 DC N1 N N N 47 DC C2 C N N 48 DC O2 O N N 49 DC N3 N N N 50 DC C4 C N N 51 DC N4 N N N 52 DC C5 C N N 53 DC C6 C N N 54 DC HOP3 H N N 55 DC HOP2 H N N 56 DC "H5'" H N N 57 DC "H5''" H N N 58 DC "H4'" H N N 59 DC "H3'" H N N 60 DC "HO3'" H N N 61 DC "H2'" H N N 62 DC "H2''" H N N 63 DC "H1'" H N N 64 DC H41 H N N 65 DC H42 H N N 66 DC H5 H N N 67 DC H6 H N N 68 DG OP3 O N N 69 DG P P N N 70 DG OP1 O N N 71 DG OP2 O N N 72 DG "O5'" O N N 73 DG "C5'" C N N 74 DG "C4'" C N R 75 DG "O4'" O N N 76 DG "C3'" C N S 77 DG "O3'" O N N 78 DG "C2'" C N N 79 DG "C1'" C N R 80 DG N9 N Y N 81 DG C8 C Y N 82 DG N7 N Y N 83 DG C5 C Y N 84 DG C6 C N N 85 DG O6 O N N 86 DG N1 N N N 87 DG C2 C N N 88 DG N2 N N N 89 DG N3 N N N 90 DG C4 C Y N 91 DG HOP3 H N N 92 DG HOP2 H N N 93 DG "H5'" H N N 94 DG "H5''" H N N 95 DG "H4'" H N N 96 DG "H3'" H N N 97 DG "HO3'" H N N 98 DG "H2'" H N N 99 DG "H2''" H N N 100 DG "H1'" H N N 101 DG H8 H N N 102 DG H1 H N N 103 DG H21 H N N 104 DG H22 H N N 105 DM8 C1 C Y N 106 DM8 C2 C Y N 107 DM8 C3 C Y N 108 DM8 C4 C Y N 109 DM8 C5 C N N 110 DM8 C6 C Y N 111 DM8 C7 C N S 112 DM8 C8 C N N 113 DM8 C9 C N S 114 DM8 C10 C N N 115 DM8 C11 C Y N 116 DM8 C12 C N N 117 DM8 C13 C N N 118 DM8 C14 C N N 119 DM8 C15 C Y N 120 DM8 C16 C Y N 121 DM8 C17 C Y N 122 DM8 C18 C Y N 123 DM8 C19 C Y N 124 DM8 C20 C Y N 125 DM8 C21 C N N 126 DM8 O4 O N N 127 DM8 O5 O N N 128 DM8 O6 O N N 129 DM8 O7 O N N 130 DM8 O9 O N N 131 DM8 O11 O N N 132 DM8 O12 O N N 133 DM8 O13 O N N 134 DM8 "C1'" C N R 135 DM8 "C2'" C N R 136 DM8 "C3'" C N R 137 DM8 "C4'" C N R 138 DM8 "C5'" C N S 139 DM8 "C6'" C N N 140 DM8 "O5'" O N N 141 DM8 "O4'" O N N 142 DM8 "N3'" N N N 143 DM8 BR BR N N 144 DM8 H1 H N N 145 DM8 H2 H N N 146 DM8 H3 H N N 147 DM8 H7 H N N 148 DM8 H81 H N N 149 DM8 H82 H N N 150 DM8 H101 H N N 151 DM8 H102 H N N 152 DM8 H141 H N N 153 DM8 H142 H N N 154 DM8 H143 H N N 155 DM8 H211 H N N 156 DM8 H212 H N N 157 DM8 H213 H N N 158 DM8 H6 H N N 159 DM8 H9 H N N 160 DM8 H11 H N N 161 DM8 "H1'" H N N 162 DM8 "H2'" H N N 163 DM8 "H3'" H N N 164 DM8 "H4'" H N N 165 DM8 "H5'" H N N 166 DM8 "H6'1" H N N 167 DM8 "H6'2" H N N 168 DM8 "H6'3" H N N 169 DM8 "HO4'" H N N 170 DM8 "HN'1" H N N 171 DM8 "HN'2" H N N 172 G49 P P N N 173 G49 O1P O N N 174 G49 O2P O N N 175 G49 O3P O N N 176 G49 "O5'" O N N 177 G49 "C5'" C N N 178 G49 "C4'" C N R 179 G49 "O4'" O N N 180 G49 "C3'" C N S 181 G49 "O3'" O N N 182 G49 "C2'" C N N 183 G49 "C1'" C N R 184 G49 N9 N Y N 185 G49 C8 C Y N 186 G49 N7 N Y N 187 G49 C5 C Y N 188 G49 C6 C N N 189 G49 O6 O N N 190 G49 N1 N N N 191 G49 C2 C N N 192 G49 N2 N N N 193 G49 CM2 C N N 194 G49 N3 N N N 195 G49 C4 C Y N 196 G49 H2P H N N 197 G49 H3P H N N 198 G49 "H5'1" H N N 199 G49 "H5'2" H N N 200 G49 "H4'" H N N 201 G49 "H3'" H N N 202 G49 HA H N N 203 G49 "H2'1" H N N 204 G49 "H2'2" H N N 205 G49 "H1'" H N N 206 G49 H8 H N N 207 G49 H1 H N N 208 G49 H2 H N N 209 G49 HM21 H N N 210 G49 HM22 H N N 211 G49 HM23 H N N 212 HOH O O N N 213 HOH H1 H N N 214 HOH H2 H N N 215 # 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 CBR BR C5 sing N N 1 CBR P OP1 doub N N 2 CBR P OP2 sing N N 3 CBR P "O5'" sing N N 4 CBR P OP3 sing N N 5 CBR OP2 HOP2 sing N N 6 CBR "O5'" "C5'" sing N N 7 CBR N1 C6 sing N N 8 CBR N1 C2 sing N N 9 CBR N1 "C1'" sing N N 10 CBR C6 C5 doub N N 11 CBR C6 H6 sing N N 12 CBR C2 O2 doub N N 13 CBR C2 N3 sing N N 14 CBR N3 C4 doub N N 15 CBR C4 N4 sing N N 16 CBR C4 C5 sing N N 17 CBR N4 H41 sing N N 18 CBR N4 H42 sing N N 19 CBR "C2'" "C1'" sing N N 20 CBR "C2'" "C3'" sing N N 21 CBR "C2'" "H2'" sing N N 22 CBR "C2'" "H2''" sing N N 23 CBR "C5'" "C4'" sing N N 24 CBR "C5'" "H5'" sing N N 25 CBR "C5'" "H5''" sing N N 26 CBR "C4'" "O4'" sing N N 27 CBR "C4'" "C3'" sing N N 28 CBR "C4'" "H4'" sing N N 29 CBR "O4'" "C1'" sing N N 30 CBR "C1'" "H1'" sing N N 31 CBR "C3'" "O3'" sing N N 32 CBR "C3'" "H3'" sing N N 33 CBR "O3'" "HO3'" sing N N 34 CBR OP3 HOP3 sing N N 35 DC OP3 P sing N N 36 DC OP3 HOP3 sing N N 37 DC P OP1 doub N N 38 DC P OP2 sing N N 39 DC P "O5'" sing N N 40 DC OP2 HOP2 sing N N 41 DC "O5'" "C5'" sing N N 42 DC "C5'" "C4'" sing N N 43 DC "C5'" "H5'" sing N N 44 DC "C5'" "H5''" sing N N 45 DC "C4'" "O4'" sing N N 46 DC "C4'" "C3'" sing N N 47 DC "C4'" "H4'" sing N N 48 DC "O4'" "C1'" sing N N 49 DC "C3'" "O3'" sing N N 50 DC "C3'" "C2'" sing N N 51 DC "C3'" "H3'" sing N N 52 DC "O3'" "HO3'" sing N N 53 DC "C2'" "C1'" sing N N 54 DC "C2'" "H2'" sing N N 55 DC "C2'" "H2''" sing N N 56 DC "C1'" N1 sing N N 57 DC "C1'" "H1'" sing N N 58 DC N1 C2 sing N N 59 DC N1 C6 sing N N 60 DC C2 O2 doub N N 61 DC C2 N3 sing N N 62 DC N3 C4 doub N N 63 DC C4 N4 sing N N 64 DC C4 C5 sing N N 65 DC N4 H41 sing N N 66 DC N4 H42 sing N N 67 DC C5 C6 doub N N 68 DC C5 H5 sing N N 69 DC C6 H6 sing N N 70 DG OP3 P sing N N 71 DG OP3 HOP3 sing N N 72 DG P OP1 doub N N 73 DG P OP2 sing N N 74 DG P "O5'" sing N N 75 DG OP2 HOP2 sing N N 76 DG "O5'" "C5'" sing N N 77 DG "C5'" "C4'" sing N N 78 DG "C5'" "H5'" sing N N 79 DG "C5'" "H5''" sing N N 80 DG "C4'" "O4'" sing N N 81 DG "C4'" "C3'" sing N N 82 DG "C4'" "H4'" sing N N 83 DG "O4'" "C1'" sing N N 84 DG "C3'" "O3'" sing N N 85 DG "C3'" "C2'" sing N N 86 DG "C3'" "H3'" sing N N 87 DG "O3'" "HO3'" sing N N 88 DG "C2'" "C1'" sing N N 89 DG "C2'" "H2'" sing N N 90 DG "C2'" "H2''" sing N N 91 DG "C1'" N9 sing N N 92 DG "C1'" "H1'" sing N N 93 DG N9 C8 sing Y N 94 DG N9 C4 sing Y N 95 DG C8 N7 doub Y N 96 DG C8 H8 sing N N 97 DG N7 C5 sing Y N 98 DG C5 C6 sing N N 99 DG C5 C4 doub Y N 100 DG C6 O6 doub N N 101 DG C6 N1 sing N N 102 DG N1 C2 sing N N 103 DG N1 H1 sing N N 104 DG C2 N2 sing N N 105 DG C2 N3 doub N N 106 DG N2 H21 sing N N 107 DG N2 H22 sing N N 108 DG N3 C4 sing N N 109 DM8 C1 C2 doub Y N 110 DM8 C1 C15 sing Y N 111 DM8 C1 H1 sing N N 112 DM8 C2 C3 sing Y N 113 DM8 C2 H2 sing N N 114 DM8 C3 C4 doub Y N 115 DM8 C3 H3 sing N N 116 DM8 C4 C16 sing Y N 117 DM8 C4 O4 sing N N 118 DM8 C5 C16 sing N N 119 DM8 C5 C17 sing N N 120 DM8 C5 O5 doub N N 121 DM8 C6 C17 doub Y N 122 DM8 C6 C20 sing Y N 123 DM8 C6 O6 sing N N 124 DM8 C7 C8 sing N N 125 DM8 C7 C20 sing N N 126 DM8 C7 O7 sing N N 127 DM8 C7 H7 sing N N 128 DM8 C8 C9 sing N N 129 DM8 C8 H81 sing N N 130 DM8 C8 H82 sing N N 131 DM8 C9 C10 sing N N 132 DM8 C9 C13 sing N N 133 DM8 C9 O9 sing N N 134 DM8 C10 C19 sing N N 135 DM8 C10 H101 sing N N 136 DM8 C10 H102 sing N N 137 DM8 C11 C18 doub Y N 138 DM8 C11 C19 sing Y N 139 DM8 C11 O11 sing N N 140 DM8 C12 C15 sing N N 141 DM8 C12 C18 sing N N 142 DM8 C12 O12 doub N N 143 DM8 C13 C14 sing N N 144 DM8 C13 O13 doub N N 145 DM8 C14 H141 sing N N 146 DM8 C14 H142 sing N N 147 DM8 C14 H143 sing N N 148 DM8 C15 C16 doub Y N 149 DM8 C17 C18 sing Y N 150 DM8 C19 C20 doub Y N 151 DM8 C21 O4 sing N N 152 DM8 C21 H211 sing N N 153 DM8 C21 H212 sing N N 154 DM8 C21 H213 sing N N 155 DM8 O6 H6 sing N N 156 DM8 O7 "C1'" sing N N 157 DM8 O9 H9 sing N N 158 DM8 O11 H11 sing N N 159 DM8 "C1'" "C2'" sing N N 160 DM8 "C1'" "O5'" sing N N 161 DM8 "C1'" "H1'" sing N N 162 DM8 "C2'" "C3'" sing N N 163 DM8 "C2'" BR sing N N 164 DM8 "C2'" "H2'" sing N N 165 DM8 "C3'" "C4'" sing N N 166 DM8 "C3'" "N3'" sing N N 167 DM8 "C3'" "H3'" sing N N 168 DM8 "C4'" "C5'" sing N N 169 DM8 "C4'" "O4'" sing N N 170 DM8 "C4'" "H4'" sing N N 171 DM8 "C5'" "C6'" sing N N 172 DM8 "C5'" "O5'" sing N N 173 DM8 "C5'" "H5'" sing N N 174 DM8 "C6'" "H6'1" sing N N 175 DM8 "C6'" "H6'2" sing N N 176 DM8 "C6'" "H6'3" sing N N 177 DM8 "O4'" "HO4'" sing N N 178 DM8 "N3'" "HN'1" sing N N 179 DM8 "N3'" "HN'2" sing N N 180 G49 P O1P doub N N 181 G49 P O2P sing N N 182 G49 P O3P sing N N 183 G49 P "O5'" sing N N 184 G49 O2P H2P sing N N 185 G49 O3P H3P sing N N 186 G49 "O5'" "C5'" sing N N 187 G49 "C5'" "C4'" sing N N 188 G49 "C5'" "H5'1" sing N N 189 G49 "C5'" "H5'2" sing N N 190 G49 "C4'" "O4'" sing N N 191 G49 "C4'" "C3'" sing N N 192 G49 "C4'" "H4'" sing N N 193 G49 "O4'" "C1'" sing N N 194 G49 "C3'" "O3'" sing N N 195 G49 "C3'" "C2'" sing N N 196 G49 "C3'" "H3'" sing N N 197 G49 "O3'" HA sing N N 198 G49 "C2'" "C1'" sing N N 199 G49 "C2'" "H2'1" sing N N 200 G49 "C2'" "H2'2" sing N N 201 G49 "C1'" N9 sing N N 202 G49 "C1'" "H1'" sing N N 203 G49 N9 C8 sing Y N 204 G49 N9 C4 sing Y N 205 G49 C8 N7 doub Y N 206 G49 C8 H8 sing N N 207 G49 N7 C5 sing Y N 208 G49 C5 C6 sing N N 209 G49 C5 C4 doub Y N 210 G49 C6 O6 doub N N 211 G49 C6 N1 sing N N 212 G49 N1 C2 sing N N 213 G49 N1 H1 sing N N 214 G49 C2 N2 sing N N 215 G49 C2 N3 doub N N 216 G49 N2 CM2 sing N N 217 G49 N2 H2 sing N N 218 G49 CM2 HM21 sing N N 219 G49 CM2 HM22 sing N N 220 G49 CM2 HM23 sing N N 221 G49 N3 C4 sing N N 222 HOH O H1 sing N N 223 HOH O H2 sing N N 224 # _ndb_struct_conf_na.entry_id 380D _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 6 1_555 0.412 -0.181 -0.091 8.443 -0.526 -3.206 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 -0.299 -0.223 -0.266 -11.083 5.491 1.023 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A G49 3 1_555 B CBR 4 1_555 -0.246 -0.118 0.157 -3.549 -4.757 -0.377 3 A_G493:CBR10_B A 3 ? B 10 ? 19 1 1 A CBR 4 1_555 B G49 3 1_555 0.228 -0.091 0.072 5.293 -6.882 -2.112 4 A_CBR4:G499_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B DG 2 1_555 0.159 -0.087 -0.504 18.930 5.188 2.866 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 -0.346 -0.219 -0.130 -6.668 4.864 -0.332 6 A_DG6:DC7_B A 6 ? B 7 ? 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 6 1_555 A DG 2 1_555 B DC 5 1_555 1.257 1.271 6.930 0.686 -4.677 32.428 3.941 -1.982 6.710 -8.319 -1.220 32.762 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 5 1_555 A G49 3 1_555 B CBR 4 1_555 -1.471 0.835 3.278 -5.418 1.061 32.884 1.272 1.625 3.493 1.858 9.487 33.332 2 AA_DG2G493:CBR10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A G49 3 1_555 B CBR 4 1_555 A CBR 4 1_555 B G49 3 1_555 0.008 -0.658 3.191 1.174 0.660 33.312 -1.254 0.177 3.176 1.151 -2.048 33.338 3 AA_G493CBR4:G499CBR10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A CBR 4 1_555 B G49 3 1_555 A DC 5 1_555 B DG 2 1_555 1.540 0.854 3.030 7.249 1.790 31.927 1.210 -1.501 3.331 3.199 -12.958 32.766 4 AA_CBR4DC5:DG8G499_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -1.104 1.289 7.102 -4.054 -4.294 32.356 3.869 0.449 6.961 -7.627 7.200 32.876 5 AA_DC5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _atom_sites.entry_id 380D _atom_sites.fract_transf_matrix[1][1] 0.026860 _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] 0.026860 _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] 0.016139 _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 BR C N O P # loop_