data_3GJH # _entry.id 3GJH # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 3GJH pdb_00003gjh 10.2210/pdb3gjh/pdb NDB DD104 ? ? RCSB RCSB051937 ? ? WWPDB D_1000051937 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3GJJ . unspecified PDB 3GJK . unspecified PDB 3GJL . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3GJH _pdbx_database_status.recvd_initial_deposition_date 2009-03-09 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _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 'Takenaka, A.' 1 'Juan, E.C.M.' 2 'Shimizu, S.' 3 'Haraguchi, T.' 4 'Xiao, M.' 5 'Kurose, T.' 6 # _citation.id primary _citation.title ;Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one ; _citation.journal_abbrev 'To be Published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Takenaka, A.' 1 ? primary 'Juan, E.C.M.' 2 ? primary 'Shimizu, S.' 3 ? primary 'Haraguchi, T.' 4 ? primary 'Xiao, M.' 5 ? primary 'Kurose, T.' 6 ? primary 'Ohkubo, A.' 7 ? primary 'Sekine, M.' 8 ? primary 'Shibata, T.' 9 ? primary 'Millington, C.L.' 10 ? # _cell.entry_id 3GJH _cell.length_a 25.207 _cell.length_b 41.379 _cell.length_c 64.866 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3GJH _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 _symmetry.space_group_name_Hall ? # 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 "5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3'" 3701.440 2 ? ? ? ? 2 non-polymer syn '6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE' 277.324 1 ? ? ? ? 3 water nat water 18.015 16 ? ? ? ? # _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)(DC)(DG)(DA)(DA)(DT)(DT)(B7C)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTXGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # 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 B7C n 1 10 DG n 1 11 DC n 1 12 DG n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3GJH _struct_ref.pdbx_db_accession 3GJH _struct_ref.entity_id 1 _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 3GJH A 1 ? 12 ? 3GJH 1 ? 12 ? 1 12 2 1 3GJH B 1 ? 12 ? 3GJH 13 ? 24 ? 13 24 # 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 B7C 'DNA linking' n '3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydropyrido[2,3-d]pyrimidin-2(3H)-one' ? 'C12 H16 N3 O7 P' 345.245 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DAP non-polymer . '6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE' ? 'C16 H15 N5' 277.324 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 # _exptl.entry_id 3GJH _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.28 _exptl_crystal.density_percent_sol 46.17 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;20mM Sodium cacodylate (pH7.0), 6mM Spermine tetrahydrochloride, 40mM KCl, 0.2% CHAPSO, 0.30mM DAPI, 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2007-12-16 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE AR-NW12A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline AR-NW12A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.entry_id 3GJH _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.9 _reflns.number_obs 1708 _reflns.number_all 1708 _reflns.percent_possible_obs 98.9 _reflns.pdbx_Rmerge_I_obs 0.064 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 38.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.1 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.90 _reflns_shell.d_res_low 3.00 _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs 0.322 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.5 _reflns_shell.pdbx_redundancy 4.2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3GJH _refine.ls_number_reflns_obs 1629 _refine.ls_number_reflns_all 1689 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0 _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 _refine.ls_d_res_high 2.9 _refine.ls_percent_reflns_obs 99.3 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.259 _refine.ls_R_factor_R_free 0.306 _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 157 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 43.9 _refine.aniso_B[1][1] 0 _refine.aniso_B[2][2] 0 _refine.aniso_B[3][3] 0 _refine.aniso_B[1][2] 0 _refine.aniso_B[1][3] 0 _refine.aniso_B[2][3] 0 _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'Used weighted full matrix least squares procedure' _refine.pdbx_starting_model 1D30 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Anisotropic _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details Random _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _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 492 _refine_hist.pdbx_number_atoms_ligand 21 _refine_hist.number_atoms_solvent 16 _refine_hist.number_atoms_total 529 _refine_hist.d_res_high 2.9 _refine_hist.d_res_low 10 # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.90 _refine_ls_shell.d_res_low 3.08 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.578 _refine_ls_shell.percent_reflns_obs 95.9 _refine_ls_shell.R_factor_R_free 0.597 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 31 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 228 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3GJH _struct.title 'Crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3GJH _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA duplex, bicyclic cytosine, 7, 8-dihydropyridol[2, 3-d]pyrimidin-2-one, 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_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 DT 8 "O3'" ? ? ? 1_555 A B7C 9 P ? ? A DT 8 A B7C 9 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale2 covale both ? A B7C 9 "O3'" ? ? ? 1_555 A DG 10 P ? ? A B7C 9 A DG 10 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale3 covale both ? B DT 8 "O3'" ? ? ? 1_555 B B7C 9 P ? ? B DT 20 B B7C 21 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? B B7C 9 "O3'" ? ? ? 1_555 B DG 10 P ? ? B B7C 21 B DG 22 1_555 ? ? ? ? ? ? ? 1.606 ? ? 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 B7C 9 N3 ? ? A DG 4 B B7C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B B7C 9 O2 ? ? A DG 4 B B7C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B B7C 9 N4 ? ? A DG 4 B B7C 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 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A B7C 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A B7C 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A B7C 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A B7C 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A B7C 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A B7C 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 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 B DAP 25 ? 10 'BINDING SITE FOR RESIDUE DAP B 25' 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 10 DT A 7 ? DT A 7 . ? 1_555 ? 2 AC1 10 DT A 8 ? DT A 8 . ? 1_555 ? 3 AC1 10 B7C A 9 ? B7C A 9 . ? 1_555 ? 4 AC1 10 DG A 10 ? DG A 10 . ? 1_555 ? 5 AC1 10 HOH E . ? HOH B 3 . ? 1_555 ? 6 AC1 10 DA B 5 ? DA B 17 . ? 1_555 ? 7 AC1 10 DA B 6 ? DA B 18 . ? 1_555 ? 8 AC1 10 DT B 7 ? DT B 19 . ? 1_555 ? 9 AC1 10 DT B 8 ? DT B 20 . ? 1_555 ? 10 AC1 10 B7C B 9 ? B7C B 21 . ? 1_555 ? # _database_PDB_matrix.entry_id 3GJH _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 # _atom_sites.entry_id 3GJH _atom_sites.fract_transf_matrix[1][1] 0.039672 _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] 0.024167 _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] 0.015416 _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_ _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 CYT A . n A 1 2 DG 2 2 2 DG GUA A . n A 1 3 DC 3 3 3 DC CYT A . n A 1 4 DG 4 4 4 DG GUX A . n A 1 5 DA 5 5 5 DA ADE A . n A 1 6 DA 6 6 6 DA ADE A . n A 1 7 DT 7 7 7 DT THY A . n A 1 8 DT 8 8 8 DT THY A . n A 1 9 B7C 9 9 9 B7C BIC A . n A 1 10 DG 10 10 10 DG GUA A . n A 1 11 DC 11 11 11 DC CYT A . n A 1 12 DG 12 12 12 DG GUA A . n B 1 1 DC 1 13 13 DC CYT B . n B 1 2 DG 2 14 14 DG GUA B . n B 1 3 DC 3 15 15 DC CYT B . n B 1 4 DG 4 16 16 DG GUX B . n B 1 5 DA 5 17 17 DA ADE B . n B 1 6 DA 6 18 18 DA ADE B . n B 1 7 DT 7 19 19 DT THY B . n B 1 8 DT 8 20 20 DT THY B . n B 1 9 B7C 9 21 21 B7C BIC B . n B 1 10 DG 10 22 22 DG GUA B . n B 1 11 DC 11 23 23 DC CYT B . n B 1 12 DG 12 24 24 DG GUA 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 DAP 1 25 25 DAP DAP B . D 3 HOH 1 13 2 HOH HOH A . D 3 HOH 2 14 14 HOH HOH A . D 3 HOH 3 15 4 HOH HOH A . D 3 HOH 4 16 5 HOH HOH A . D 3 HOH 5 17 7 HOH HOH A . D 3 HOH 6 18 8 HOH HOH A . D 3 HOH 7 19 9 HOH HOH A . D 3 HOH 8 20 11 HOH HOH A . E 3 HOH 1 1 1 HOH HOH B . E 3 HOH 2 3 3 HOH HOH B . E 3 HOH 3 6 6 HOH HOH B . E 3 HOH 4 10 10 HOH HOH B . E 3 HOH 5 12 12 HOH HOH B . E 3 HOH 6 26 13 HOH HOH B . E 3 HOH 7 27 15 HOH HOH B . E 3 HOH 8 28 16 HOH HOH B . # 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 B7C 9 A B7C 9 ? DC ? 2 B B7C 9 B B7C 21 ? DC ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1910 ? 1 MORE 7 ? 1 'SSA (A^2)' 4210 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 2010-03-31 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-11-01 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn 6 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 AMoRE phasing . ? 2 CNS refinement 1.1 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # 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 B7C OP3 O N N 1 B7C P P N N 2 B7C OP1 O N N 3 B7C OP2 O N N 4 B7C "O5'" O N N 5 B7C N1 N N N 6 B7C C6 C N N 7 B7C C2 C N N 8 B7C O2 O N N 9 B7C N3 N N N 10 B7C C4 C N N 11 B7C N4 N N N 12 B7C C5 C N N 13 B7C C7 C N N 14 B7C C8 C N N 15 B7C C9 C N N 16 B7C "C2'" C N N 17 B7C "C5'" C N N 18 B7C "C4'" C N R 19 B7C "O4'" O N N 20 B7C "C1'" C N R 21 B7C "C3'" C N S 22 B7C "O3'" O N N 23 B7C HOP3 H N N 24 B7C HOP1 H N N 25 B7C H6 H N N 26 B7C HN4 H N N 27 B7C H7 H N N 28 B7C H8 H N N 29 B7C H9 H N N 30 B7C H9A H N N 31 B7C "H2'" H N N 32 B7C "H2'A" H N N 33 B7C "H5'" H N N 34 B7C "H5'A" H N N 35 B7C "H4'" H N N 36 B7C "H1'" H N N 37 B7C "H3'" H N N 38 B7C "HO3'" H N N 39 DA OP3 O N N 40 DA P P N N 41 DA OP1 O N N 42 DA OP2 O N N 43 DA "O5'" O N N 44 DA "C5'" C N N 45 DA "C4'" C N R 46 DA "O4'" O N N 47 DA "C3'" C N S 48 DA "O3'" O N N 49 DA "C2'" C N N 50 DA "C1'" C N R 51 DA N9 N Y N 52 DA C8 C Y N 53 DA N7 N Y N 54 DA C5 C Y N 55 DA C6 C Y N 56 DA N6 N N N 57 DA N1 N Y N 58 DA C2 C Y N 59 DA N3 N Y N 60 DA C4 C Y N 61 DA HOP3 H N N 62 DA HOP2 H N N 63 DA "H5'" H N N 64 DA "H5''" H N N 65 DA "H4'" H N N 66 DA "H3'" H N N 67 DA "HO3'" H N N 68 DA "H2'" H N N 69 DA "H2''" H N N 70 DA "H1'" H N N 71 DA H8 H N N 72 DA H61 H N N 73 DA H62 H N N 74 DA H2 H N N 75 DAP N1 N Y N 76 DAP C2 C Y N 77 DAP C3 C Y N 78 DAP C4 C Y N 79 DAP C5 C Y N 80 DAP C6 C Y N 81 DAP C7 C Y N 82 DAP C8 C Y N 83 DAP C9 C Y N 84 DAP C10 C N N 85 DAP N2 N N N 86 DAP N3 N N N 87 DAP "C1'" C Y N 88 DAP "C2'" C Y N 89 DAP "C3'" C Y N 90 DAP "C4'" C Y N 91 DAP "C5'" C Y N 92 DAP "C6'" C Y N 93 DAP C11 C N N 94 DAP N4 N N N 95 DAP N5 N N N 96 DAP HN1 H N N 97 DAP H3 H N N 98 DAP H4 H N N 99 DAP H5 H N N 100 DAP H7 H N N 101 DAP HN2 H N N 102 DAP HN31 H N N 103 DAP HN32 H N N 104 DAP "H2'" H N N 105 DAP "H3'" H N N 106 DAP "H5'" H N N 107 DAP "H6'" H N N 108 DAP HN4 H N N 109 DAP HN51 H N N 110 DAP HN52 H N N 111 DC OP3 O N N 112 DC P P N N 113 DC OP1 O N N 114 DC OP2 O N N 115 DC "O5'" O N N 116 DC "C5'" C N N 117 DC "C4'" C N R 118 DC "O4'" O N N 119 DC "C3'" C N S 120 DC "O3'" O N N 121 DC "C2'" C N N 122 DC "C1'" C N R 123 DC N1 N N N 124 DC C2 C N N 125 DC O2 O N N 126 DC N3 N N N 127 DC C4 C N N 128 DC N4 N N N 129 DC C5 C N N 130 DC C6 C N N 131 DC HOP3 H N N 132 DC HOP2 H N N 133 DC "H5'" H N N 134 DC "H5''" H N N 135 DC "H4'" H N N 136 DC "H3'" H N N 137 DC "HO3'" H N N 138 DC "H2'" H N N 139 DC "H2''" H N N 140 DC "H1'" H N N 141 DC H41 H N N 142 DC H42 H N N 143 DC H5 H N N 144 DC H6 H N N 145 DG OP3 O N N 146 DG P P N N 147 DG OP1 O N N 148 DG OP2 O N N 149 DG "O5'" O N N 150 DG "C5'" C N N 151 DG "C4'" C N R 152 DG "O4'" O N N 153 DG "C3'" C N S 154 DG "O3'" O N N 155 DG "C2'" C N N 156 DG "C1'" C N R 157 DG N9 N Y N 158 DG C8 C Y N 159 DG N7 N Y N 160 DG C5 C Y N 161 DG C6 C N N 162 DG O6 O N N 163 DG N1 N N N 164 DG C2 C N N 165 DG N2 N N N 166 DG N3 N N N 167 DG C4 C Y N 168 DG HOP3 H N N 169 DG HOP2 H N N 170 DG "H5'" H N N 171 DG "H5''" H N N 172 DG "H4'" H N N 173 DG "H3'" H N N 174 DG "HO3'" H N N 175 DG "H2'" H N N 176 DG "H2''" H N N 177 DG "H1'" H N N 178 DG H8 H N N 179 DG H1 H N N 180 DG H21 H N N 181 DG H22 H N N 182 DT OP3 O N N 183 DT P P N N 184 DT OP1 O N N 185 DT OP2 O N N 186 DT "O5'" O N N 187 DT "C5'" C N N 188 DT "C4'" C N R 189 DT "O4'" O N N 190 DT "C3'" C N S 191 DT "O3'" O N N 192 DT "C2'" C N N 193 DT "C1'" C N R 194 DT N1 N N N 195 DT C2 C N N 196 DT O2 O N N 197 DT N3 N N N 198 DT C4 C N N 199 DT O4 O N N 200 DT C5 C N N 201 DT C7 C N N 202 DT C6 C N N 203 DT HOP3 H N N 204 DT HOP2 H N N 205 DT "H5'" H N N 206 DT "H5''" H N N 207 DT "H4'" H N N 208 DT "H3'" H N N 209 DT "HO3'" H N N 210 DT "H2'" H N N 211 DT "H2''" H N N 212 DT "H1'" H N N 213 DT H3 H N N 214 DT H71 H N N 215 DT H72 H N N 216 DT H73 H N N 217 DT H6 H N N 218 HOH O O N N 219 HOH H1 H N N 220 HOH H2 H N N 221 # 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 B7C OP3 P sing N N 1 B7C P OP1 sing N N 2 B7C P OP2 doub N N 3 B7C P "O5'" sing N N 4 B7C "O5'" "C5'" sing N N 5 B7C N1 C6 sing N N 6 B7C N1 C2 sing N N 7 B7C N1 "C1'" sing N N 8 B7C C6 C5 doub N N 9 B7C C2 O2 doub N N 10 B7C C2 N3 sing N N 11 B7C N3 C4 doub N N 12 B7C C4 N4 sing N N 13 B7C C4 C5 sing N N 14 B7C N4 C9 sing N N 15 B7C C5 C7 sing N N 16 B7C C7 C8 doub N N 17 B7C C8 C9 sing N N 18 B7C "C2'" "C1'" sing N N 19 B7C "C2'" "C3'" sing N N 20 B7C "C5'" "C4'" sing N N 21 B7C "C4'" "O4'" sing N N 22 B7C "C4'" "C3'" sing N N 23 B7C "O4'" "C1'" sing N N 24 B7C "C3'" "O3'" sing N N 25 B7C OP3 HOP3 sing N N 26 B7C OP1 HOP1 sing N N 27 B7C C6 H6 sing N N 28 B7C N4 HN4 sing N N 29 B7C C7 H7 sing N N 30 B7C C8 H8 sing N N 31 B7C C9 H9 sing N N 32 B7C C9 H9A sing N N 33 B7C "C2'" "H2'" sing N N 34 B7C "C2'" "H2'A" sing N N 35 B7C "C5'" "H5'" sing N N 36 B7C "C5'" "H5'A" sing N N 37 B7C "C4'" "H4'" sing N N 38 B7C "C1'" "H1'" sing N N 39 B7C "C3'" "H3'" sing N N 40 B7C "O3'" "HO3'" sing N N 41 DA OP3 P sing N N 42 DA OP3 HOP3 sing N N 43 DA P OP1 doub N N 44 DA P OP2 sing N N 45 DA P "O5'" sing N N 46 DA OP2 HOP2 sing N N 47 DA "O5'" "C5'" sing N N 48 DA "C5'" "C4'" sing N N 49 DA "C5'" "H5'" sing N N 50 DA "C5'" "H5''" sing N N 51 DA "C4'" "O4'" sing N N 52 DA "C4'" "C3'" sing N N 53 DA "C4'" "H4'" sing N N 54 DA "O4'" "C1'" sing N N 55 DA "C3'" "O3'" sing N N 56 DA "C3'" "C2'" sing N N 57 DA "C3'" "H3'" sing N N 58 DA "O3'" "HO3'" sing N N 59 DA "C2'" "C1'" sing N N 60 DA "C2'" "H2'" sing N N 61 DA "C2'" "H2''" sing N N 62 DA "C1'" N9 sing N N 63 DA "C1'" "H1'" sing N N 64 DA N9 C8 sing Y N 65 DA N9 C4 sing Y N 66 DA C8 N7 doub Y N 67 DA C8 H8 sing N N 68 DA N7 C5 sing Y N 69 DA C5 C6 sing Y N 70 DA C5 C4 doub Y N 71 DA C6 N6 sing N N 72 DA C6 N1 doub Y N 73 DA N6 H61 sing N N 74 DA N6 H62 sing N N 75 DA N1 C2 sing Y N 76 DA C2 N3 doub Y N 77 DA C2 H2 sing N N 78 DA N3 C4 sing Y N 79 DAP N1 C2 sing Y N 80 DAP N1 C8 sing Y N 81 DAP N1 HN1 sing N N 82 DAP C2 C3 doub Y N 83 DAP C2 "C1'" sing Y N 84 DAP C3 C9 sing Y N 85 DAP C3 H3 sing N N 86 DAP C4 C5 doub Y N 87 DAP C4 C9 sing Y N 88 DAP C4 H4 sing N N 89 DAP C5 C6 sing Y N 90 DAP C5 H5 sing N N 91 DAP C6 C7 doub Y N 92 DAP C6 C10 sing N N 93 DAP C7 C8 sing Y N 94 DAP C7 H7 sing N N 95 DAP C8 C9 doub Y N 96 DAP C10 N2 doub N N 97 DAP C10 N3 sing N N 98 DAP N2 HN2 sing N N 99 DAP N3 HN31 sing N N 100 DAP N3 HN32 sing N N 101 DAP "C1'" "C2'" doub Y N 102 DAP "C1'" "C6'" sing Y N 103 DAP "C2'" "C3'" sing Y N 104 DAP "C2'" "H2'" sing N N 105 DAP "C3'" "C4'" doub Y N 106 DAP "C3'" "H3'" sing N N 107 DAP "C4'" "C5'" sing Y N 108 DAP "C4'" C11 sing N N 109 DAP "C5'" "C6'" doub Y N 110 DAP "C5'" "H5'" sing N N 111 DAP "C6'" "H6'" sing N N 112 DAP C11 N4 doub N N 113 DAP C11 N5 sing N N 114 DAP N4 HN4 sing N N 115 DAP N5 HN51 sing N N 116 DAP N5 HN52 sing N N 117 DC OP3 P sing N N 118 DC OP3 HOP3 sing N N 119 DC P OP1 doub N N 120 DC P OP2 sing N N 121 DC P "O5'" sing N N 122 DC OP2 HOP2 sing N N 123 DC "O5'" "C5'" sing N N 124 DC "C5'" "C4'" sing N N 125 DC "C5'" "H5'" sing N N 126 DC "C5'" "H5''" sing N N 127 DC "C4'" "O4'" sing N N 128 DC "C4'" "C3'" sing N N 129 DC "C4'" "H4'" sing N N 130 DC "O4'" "C1'" sing N N 131 DC "C3'" "O3'" sing N N 132 DC "C3'" "C2'" sing N N 133 DC "C3'" "H3'" sing N N 134 DC "O3'" "HO3'" sing N N 135 DC "C2'" "C1'" sing N N 136 DC "C2'" "H2'" sing N N 137 DC "C2'" "H2''" sing N N 138 DC "C1'" N1 sing N N 139 DC "C1'" "H1'" sing N N 140 DC N1 C2 sing N N 141 DC N1 C6 sing N N 142 DC C2 O2 doub N N 143 DC C2 N3 sing N N 144 DC N3 C4 doub N N 145 DC C4 N4 sing N N 146 DC C4 C5 sing N N 147 DC N4 H41 sing N N 148 DC N4 H42 sing N N 149 DC C5 C6 doub N N 150 DC C5 H5 sing N N 151 DC C6 H6 sing N N 152 DG OP3 P sing N N 153 DG OP3 HOP3 sing N N 154 DG P OP1 doub N N 155 DG P OP2 sing N N 156 DG P "O5'" sing N N 157 DG OP2 HOP2 sing N N 158 DG "O5'" "C5'" sing N N 159 DG "C5'" "C4'" sing N N 160 DG "C5'" "H5'" sing N N 161 DG "C5'" "H5''" sing N N 162 DG "C4'" "O4'" sing N N 163 DG "C4'" "C3'" sing N N 164 DG "C4'" "H4'" sing N N 165 DG "O4'" "C1'" sing N N 166 DG "C3'" "O3'" sing N N 167 DG "C3'" "C2'" sing N N 168 DG "C3'" "H3'" sing N N 169 DG "O3'" "HO3'" sing N N 170 DG "C2'" "C1'" sing N N 171 DG "C2'" "H2'" sing N N 172 DG "C2'" "H2''" sing N N 173 DG "C1'" N9 sing N N 174 DG "C1'" "H1'" sing N N 175 DG N9 C8 sing Y N 176 DG N9 C4 sing Y N 177 DG C8 N7 doub Y N 178 DG C8 H8 sing N N 179 DG N7 C5 sing Y N 180 DG C5 C6 sing N N 181 DG C5 C4 doub Y N 182 DG C6 O6 doub N N 183 DG C6 N1 sing N N 184 DG N1 C2 sing N N 185 DG N1 H1 sing N N 186 DG C2 N2 sing N N 187 DG C2 N3 doub N N 188 DG N2 H21 sing N N 189 DG N2 H22 sing N N 190 DG N3 C4 sing N N 191 DT OP3 P sing N N 192 DT OP3 HOP3 sing N N 193 DT P OP1 doub N N 194 DT P OP2 sing N N 195 DT P "O5'" sing N N 196 DT OP2 HOP2 sing N N 197 DT "O5'" "C5'" sing N N 198 DT "C5'" "C4'" sing N N 199 DT "C5'" "H5'" sing N N 200 DT "C5'" "H5''" sing N N 201 DT "C4'" "O4'" sing N N 202 DT "C4'" "C3'" sing N N 203 DT "C4'" "H4'" sing N N 204 DT "O4'" "C1'" sing N N 205 DT "C3'" "O3'" sing N N 206 DT "C3'" "C2'" sing N N 207 DT "C3'" "H3'" sing N N 208 DT "O3'" "HO3'" sing N N 209 DT "C2'" "C1'" sing N N 210 DT "C2'" "H2'" sing N N 211 DT "C2'" "H2''" sing N N 212 DT "C1'" N1 sing N N 213 DT "C1'" "H1'" sing N N 214 DT N1 C2 sing N N 215 DT N1 C6 sing N N 216 DT C2 O2 doub N N 217 DT C2 N3 sing N N 218 DT N3 C4 sing N N 219 DT N3 H3 sing N N 220 DT C4 O4 doub N N 221 DT C4 C5 sing N N 222 DT C5 C7 sing N N 223 DT C5 C6 doub N N 224 DT C7 H71 sing N N 225 DT C7 H72 sing N N 226 DT C7 H73 sing N N 227 DT C6 H6 sing N N 228 HOH O H1 sing N N 229 HOH O H2 sing N N 230 # _ndb_struct_conf_na.entry_id 3GJH _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 0.113 -0.167 0.064 3.373 -7.019 -5.147 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.201 -0.239 0.260 0.407 -1.719 -2.556 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 -0.202 -0.002 -0.026 -5.373 3.523 -1.965 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B B7C 9 1_555 -0.108 -0.263 -0.290 7.903 -8.200 -2.544 4 A_DG4:B7C21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.102 -0.184 0.222 8.287 -8.824 2.368 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.142 -0.193 -0.023 5.457 -16.108 5.418 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.076 -0.227 0.254 -1.572 -16.464 5.760 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 0.226 -0.233 0.253 -6.619 -10.802 2.409 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A B7C 9 1_555 B DG 4 1_555 0.248 -0.102 0.045 -6.725 -4.081 0.617 9 A_B7C9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 0.081 -0.204 0.211 0.409 1.328 -1.083 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 -0.007 -0.208 0.689 -7.835 -7.803 -4.033 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.081 -0.112 0.319 0.504 -2.488 -6.058 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 0.470 0.232 3.326 2.164 5.286 33.088 -0.489 -0.449 3.346 9.197 -3.765 33.564 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 0.395 0.015 3.496 2.336 -1.633 35.946 0.273 -0.284 3.510 -2.640 -3.777 36.055 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 B7C 9 1_555 -0.537 0.558 3.162 3.002 5.693 34.423 0.093 1.333 3.155 9.516 -5.018 35.001 3 AA_DC3DG4:B7C21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B B7C 9 1_555 A DA 5 1_555 B DT 8 1_555 0.098 -0.063 3.241 -4.896 0.902 36.333 -0.222 -0.819 3.199 1.439 7.806 36.661 4 AA_DG4DA5:DT20B7C21_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 -0.100 -0.123 3.354 1.052 3.361 38.205 -0.617 0.287 3.328 5.121 -1.603 38.361 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 -0.072 -0.586 3.369 -3.588 -3.316 32.238 -0.444 -0.521 3.398 -5.929 6.416 32.596 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 0.049 -0.174 3.384 1.432 0.434 35.894 -0.347 0.133 3.381 0.704 -2.323 35.924 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 B7C 9 1_555 B DG 4 1_555 0.044 -0.281 3.235 2.629 -2.380 37.758 -0.131 0.266 3.242 -3.668 -4.051 37.918 8 AA_DT8B7C9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A B7C 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.346 0.536 3.198 -2.575 2.948 32.966 0.454 -1.030 3.197 5.173 4.517 33.191 9 AA_B7C9DG10: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 -0.910 0.609 3.636 -4.758 -6.754 37.463 1.869 0.723 3.562 -10.362 7.300 38.331 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 -0.518 0.518 3.127 0.724 1.275 39.632 0.621 0.844 3.131 1.880 -1.067 39.658 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE' DAP 3 water HOH # _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.accession_code 1D30 _pdbx_initial_refinement_model.details ? #