data_8DHC # _entry.id 8DHC # _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 8DHC pdb_00008dhc 10.2210/pdb8dhc/pdb WWPDB D_1000265927 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8DHC _pdbx_database_status.recvd_initial_deposition_date 2022-06-27 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Yatsunyk, L.A.' 1 0000-0003-3946-0939 'Li, K.S.' 2 0000-0002-1339-7380 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country GE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_id_ASTM ACIEAY _citation.journal_id_CSD 0179 _citation.journal_id_ISSN 1521-3773 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 62 _citation.language ? _citation.page_first e202301666 _citation.page_last e202301666 _citation.title 'Crystal Structure of an i-Motif from the HRAS Oncogene Promoter.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/anie.202301666 _citation.pdbx_database_id_PubMed 36995904 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Li, K.S.' 1 ? primary 'Jordan, D.' 2 ? primary 'Lin, L.Y.' 3 0000-0001-5011-1305 primary 'McCarthy, S.E.' 4 0000-0002-1063-1784 primary 'Schneekloth Jr., J.S.' 5 ? primary 'Yatsunyk, L.A.' 6 0000-0003-3946-0939 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 93.100 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 8DHC _cell.details ? _cell.formula_units_Z ? _cell.length_a 119.126 _cell.length_a_esd ? _cell.length_b 29.656 _cell.length_b_esd ? _cell.length_c 54.326 _cell.length_c_esd ? _cell.volume 191642.082 _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8DHC _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # 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 'HRAS DNA' 8145.215 2 ? ? ? ? 2 non-polymer nat '1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE' 178.226 1 ? ? ? ? 3 water nat water 18.015 7 ? ? ? ? # _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)(DC)(DC)(DG)(DT)(DG)(DC)(DC)(DC)(DT)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DC) (DA)(DA)(DC)(DC)(DC)(DG)(DA) ; _entity_poly.pdbx_seq_one_letter_code_can CGCCCGTGCCCTGCGCCCGCAACCCGA _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 DC n 1 5 DC n 1 6 DG n 1 7 DT n 1 8 DG n 1 9 DC n 1 10 DC n 1 11 DC n 1 12 DT n 1 13 DG n 1 14 DC n 1 15 DG n 1 16 DC n 1 17 DC n 1 18 DC n 1 19 DG n 1 20 DC n 1 21 DA n 1 22 DA n 1 23 DC n 1 24 DC n 1 25 DC n 1 26 DG n 1 27 DA n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 27 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8DHC _struct_ref.pdbx_db_accession 8DHC _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # 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 8DHC A 1 ? 27 ? 8DHC 1 ? 27 ? 1 27 2 1 8DHC B 1 ? 27 ? 8DHC 1 ? 27 ? 1 27 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 PG5 non-polymer . '1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE' ? 'C8 H18 O4' 178.226 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8DHC _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.85 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 56.9 _exptl_crystal.description 'rectangular prism' _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.001 M Spermine Tetrahydrochloride, 0.05 M MES pH 6.5, 17% w/v PEG 4K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 196 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M-F' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-10-25 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9791 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 24-ID-C' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9791 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-C _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 53.14 _reflns.entry_id 8DHC _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.02 _reflns.d_resolution_low 59.48 _reflns.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.number_all ? _reflns.number_obs 12489 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 97.8 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.9 _reflns.pdbx_Rmerge_I_obs 0.046 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 10.6 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.054 _reflns.pdbx_Rpim_I_all 0.027 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.997 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? _reflns.pdbx_CC_split_method ? # _reflns_shell.d_res_high 2.02 _reflns_shell.d_res_low 2.07 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 0.8 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 817 _reflns_shell.percent_possible_all 87.5 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 1.391 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 3.4 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all 0.850 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.765 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 59.10 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8DHC _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.02 _refine.ls_d_res_low 59.48 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 12296 _refine.ls_number_reflns_R_free 628 _refine.ls_number_reflns_R_work 11668 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.50 _refine.ls_percent_reflns_R_free 5.11 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2522 _refine.ls_R_factor_R_free 0.2540 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2520 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 8CXF _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 46.8033 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.3906 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 2.02 _refine_hist.d_res_low 59.48 _refine_hist.number_atoms_solvent 7 _refine_hist.number_atoms_total 1061 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1042 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0105 ? 1173 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.2280 ? 1796 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0552 ? 208 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0081 ? 52 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 33.5457 ? 520 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.02 2.23 . . 169 2832 95.76 . . . 0.5640 . 0.4810 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.23 2.55 . . 156 2934 97.66 . . . 0.4517 . 0.3789 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.55 3.21 . . 163 2910 96.64 . . . 0.4024 . 0.3283 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.21 59.48 . . 140 2992 95.96 . . . 0.1801 . 0.1999 . . . . . . . . . . . # _struct.entry_id 8DHC _struct.title 'Crystal structure of an i-motif from the HRAS promoter region' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8DHC _struct_keywords.text 'HRAS, i-Motif, DNA, oncogene' _struct_keywords.pdbx_keywords 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 ? # 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 N4 ? ? ? 1_555 B DG 2 N7 ? ? A DC 1 B DG 2 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 15 O6 ? ? A DC 1 B DG 15 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 14 N4 ? ? A DG 2 A DC 14 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog4 hydrog ? ? A DG 2 N7 ? ? ? 1_555 B DC 1 N4 ? ? A DG 2 B DC 1 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog5 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 14 N3 ? ? A DG 2 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 14 O2 ? ? A DG 2 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 14 N4 ? ? A DG 2 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DC 16 O2 ? ? A DC 3 B DC 16 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DC 16 N4 ? ? A DC 3 B DC 16 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DC 17 O2 ? ? A DC 4 B DC 17 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DC 17 N4 ? ? A DC 4 B DC 17 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog12 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DC 18 O2 ? ? A DC 5 B DC 18 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog13 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DC 18 N4 ? ? A DC 5 B DC 18 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DG 19 N3 ? ? A DG 6 B DG 19 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog15 hydrog ? ? A DG 6 N3 ? ? ? 1_555 B DG 19 N2 ? ? A DG 6 B DG 19 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog16 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DC 23 O2 ? ? A DC 9 B DC 23 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog17 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DC 23 N4 ? ? A DC 9 B DC 23 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog18 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DC 24 O2 ? ? A DC 10 B DC 24 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog19 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DC 24 N4 ? ? A DC 10 B DC 24 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog20 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DC 25 O2 ? ? A DC 11 B DC 25 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog21 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DC 25 N4 ? ? A DC 11 B DC 25 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog22 hydrog ? ? A DT 12 N3 ? ? ? 1_555 B DT 12 O2 ? ? A DT 12 B DT 12 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog23 hydrog ? ? A DT 12 O2 ? ? ? 1_555 B DT 12 N3 ? ? A DT 12 B DT 12 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog24 hydrog ? ? A DG 13 N2 ? ? ? 1_555 B DG 13 N3 ? ? A DG 13 B DG 13 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog25 hydrog ? ? A DG 13 N3 ? ? ? 1_555 B DG 13 N2 ? ? A DG 13 B DG 13 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog26 hydrog ? ? A DC 14 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 14 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 14 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 14 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 14 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 14 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 15 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 15 B DC 1 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog30 hydrog ? ? A DC 16 N4 ? ? ? 1_555 B DC 3 O2 ? ? A DC 16 B DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog31 hydrog ? ? A DC 16 O2 ? ? ? 1_555 B DC 3 N4 ? ? A DC 16 B DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog32 hydrog ? ? A DC 17 N4 ? ? ? 1_555 B DC 4 O2 ? ? A DC 17 B DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog33 hydrog ? ? A DC 17 O2 ? ? ? 1_555 B DC 4 N4 ? ? A DC 17 B DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog34 hydrog ? ? A DC 18 N4 ? ? ? 1_555 B DC 5 O2 ? ? A DC 18 B DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog35 hydrog ? ? A DC 18 O2 ? ? ? 1_555 B DC 5 N4 ? ? A DC 18 B DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog36 hydrog ? ? A DG 19 N2 ? ? ? 1_555 B DG 6 N3 ? ? A DG 19 B DG 6 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog37 hydrog ? ? A DG 19 N3 ? ? ? 1_555 B DG 6 N2 ? ? A DG 19 B DG 6 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog38 hydrog ? ? A DC 23 N4 ? ? ? 1_555 B DC 9 O2 ? ? A DC 23 B DC 9 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog39 hydrog ? ? A DC 23 O2 ? ? ? 1_555 B DC 9 N4 ? ? A DC 23 B DC 9 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog40 hydrog ? ? A DC 24 N4 ? ? ? 1_555 B DC 10 O2 ? ? A DC 24 B DC 10 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog41 hydrog ? ? A DC 24 O2 ? ? ? 1_555 B DC 10 N4 ? ? A DC 24 B DC 10 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog42 hydrog ? ? A DC 25 N4 ? ? ? 1_555 B DC 11 O2 ? ? A DC 25 B DC 11 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog43 hydrog ? ? A DC 25 O2 ? ? ? 1_555 B DC 11 N4 ? ? A DC 25 B DC 11 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog44 hydrog ? ? B DG 2 O6 ? ? ? 1_555 B DC 14 N4 ? ? B DG 2 B DC 14 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 8DHC _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.008394 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000455 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033720 _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] 0.018434 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O1- ? ? 5.12366 3.84317 ? ? 3.49406 27.47979 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # 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 DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DG 8 8 8 DG DG A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DT 12 12 12 DT DT A . n A 1 13 DG 13 13 13 DG DG A . n A 1 14 DC 14 14 14 DC DC A . n A 1 15 DG 15 15 15 DG DG A . n A 1 16 DC 16 16 16 DC DC A . n A 1 17 DC 17 17 17 DC DC A . n A 1 18 DC 18 18 18 DC DC A . n A 1 19 DG 19 19 19 DG DG A . n A 1 20 DC 20 20 20 DC DC A . n A 1 21 DA 21 21 21 DA DA A . n A 1 22 DA 22 22 22 DA DA A . n A 1 23 DC 23 23 23 DC DC A . n A 1 24 DC 24 24 24 DC DC A . n A 1 25 DC 25 25 25 DC DC A . n A 1 26 DG 26 26 26 DG DG A . n A 1 27 DA 27 27 27 DA DA A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DG 2 2 2 DG DG B . n B 1 3 DC 3 3 3 DC DC B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DC 5 5 5 DC DC B . n B 1 6 DG 6 6 6 DG DG B . n B 1 7 DT 7 7 7 DT DT B . n B 1 8 DG 8 8 8 DG DG B . n B 1 9 DC 9 9 9 DC DC B . n B 1 10 DC 10 10 10 DC DC B . n B 1 11 DC 11 11 11 DC DC B . n B 1 12 DT 12 12 12 DT DT B . n B 1 13 DG 13 13 13 DG DG B . n B 1 14 DC 14 14 14 DC DC B . n B 1 15 DG 15 15 15 DG DG B . n B 1 16 DC 16 16 16 DC DC B . n B 1 17 DC 17 17 17 DC DC B . n B 1 18 DC 18 18 18 DC DC B . n B 1 19 DG 19 19 19 DG DG B . n B 1 20 DC 20 20 20 DC DC B . n B 1 21 DA 21 21 21 DA DA B . n B 1 22 DA 22 22 22 DA DA B . n B 1 23 DC 23 23 23 DC DC B . n B 1 24 DC 24 24 24 DC DC B . n B 1 25 DC 25 25 25 DC DC B . n B 1 26 DG 26 26 26 DG DG B . n B 1 27 DA 27 27 27 DA DA B . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email lyatsun1@swarthmore.edu _pdbx_contact_author.name_first Liliya _pdbx_contact_author.name_last Yatsunyk _pdbx_contact_author.name_mi A _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-3946-0939 # 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 PG5 1 101 101 PG5 15P B . D 3 HOH 1 101 9 HOH HOH A . D 3 HOH 2 102 7 HOH HOH A . E 3 HOH 1 201 5 HOH HOH B . E 3 HOH 2 202 6 HOH HOH B . E 3 HOH 3 203 10 HOH HOH B . E 3 HOH 4 204 8 HOH HOH B . E 3 HOH 5 205 1 HOH HOH B . # _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 # 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 2023-05-10 2 'Structure model' 1 1 2023-06-28 3 'Structure model' 1 2 2023-10-25 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 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 2 'Structure model' citation 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' pdbx_initial_refinement_model # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 2 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_citation.journal_volume' # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -x,y,-z 3 x+1/2,y+1/2,z 4 -x+1/2,y+1/2,-z # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 1 ? 'model building' ? ? ? ? ? ? ? ? ? ? ? Coot ? ? ? . 2 # _pdbx_entry_details.entry_id 8DHC _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DG 13 ? ? "C3'" A DG 13 ? ? 1.382 1.419 -0.037 0.006 N 2 1 "O3'" A DC 25 ? ? "C3'" A DC 25 ? ? 1.382 1.419 -0.037 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.21 108.30 1.91 0.30 N 2 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.26 108.30 1.96 0.30 N 3 1 "O4'" A DG 26 ? ? "C1'" A DG 26 ? ? N9 A DG 26 ? ? 110.13 108.30 1.83 0.30 N 4 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 111.03 108.30 2.73 0.30 N 5 1 "O4'" B DG 26 ? ? "C1'" B DG 26 ? ? N9 B DG 26 ? ? 112.15 108.30 3.85 0.30 N # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A DC 1 ? "O5'" ? A DC 1 "O5'" 2 1 Y 1 A DA 27 ? "C5'" ? A DA 27 "C5'" 3 1 Y 1 A DA 27 ? "C4'" ? A DA 27 "C4'" 4 1 Y 1 A DA 27 ? "O4'" ? A DA 27 "O4'" 5 1 Y 1 A DA 27 ? "C3'" ? A DA 27 "C3'" 6 1 Y 1 A DA 27 ? "O3'" ? A DA 27 "O3'" 7 1 Y 1 A DA 27 ? "C2'" ? A DA 27 "C2'" 8 1 Y 1 A DA 27 ? "C1'" ? A DA 27 "C1'" 9 1 Y 1 A DA 27 ? N9 ? A DA 27 N9 10 1 Y 1 A DA 27 ? C8 ? A DA 27 C8 11 1 Y 1 A DA 27 ? N7 ? A DA 27 N7 12 1 Y 1 A DA 27 ? C5 ? A DA 27 C5 13 1 Y 1 A DA 27 ? C6 ? A DA 27 C6 14 1 Y 1 A DA 27 ? N6 ? A DA 27 N6 15 1 Y 1 A DA 27 ? N1 ? A DA 27 N1 16 1 Y 1 A DA 27 ? C2 ? A DA 27 C2 17 1 Y 1 A DA 27 ? N3 ? A DA 27 N3 18 1 Y 1 A DA 27 ? C4 ? A DA 27 C4 19 1 Y 1 B DC 1 ? "O5'" ? B DC 1 "O5'" 20 1 Y 1 B DA 27 ? "C5'" ? B DA 27 "C5'" 21 1 Y 1 B DA 27 ? "C4'" ? B DA 27 "C4'" 22 1 Y 1 B DA 27 ? "O4'" ? B DA 27 "O4'" 23 1 Y 1 B DA 27 ? "C3'" ? B DA 27 "C3'" 24 1 Y 1 B DA 27 ? "O3'" ? B DA 27 "O3'" 25 1 Y 1 B DA 27 ? "C2'" ? B DA 27 "C2'" 26 1 Y 1 B DA 27 ? "C1'" ? B DA 27 "C1'" 27 1 Y 1 B DA 27 ? N9 ? B DA 27 N9 28 1 Y 1 B DA 27 ? C8 ? B DA 27 C8 29 1 Y 1 B DA 27 ? N7 ? B DA 27 N7 30 1 Y 1 B DA 27 ? C5 ? B DA 27 C5 31 1 Y 1 B DA 27 ? C6 ? B DA 27 C6 32 1 Y 1 B DA 27 ? N6 ? B DA 27 N6 33 1 Y 1 B DA 27 ? N1 ? B DA 27 N1 34 1 Y 1 B DA 27 ? C2 ? B DA 27 C2 35 1 Y 1 B DA 27 ? N3 ? B DA 27 N3 36 1 Y 1 B DA 27 ? C4 ? B DA 27 C4 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 PG5 C1 C N N 147 PG5 O1 O N N 148 PG5 C2 C N N 149 PG5 C3 C N N 150 PG5 O2 O N N 151 PG5 C4 C N N 152 PG5 C5 C N N 153 PG5 O3 O N N 154 PG5 C6 C N N 155 PG5 C7 C N N 156 PG5 O4 O N N 157 PG5 C8 C N N 158 PG5 H11 H N N 159 PG5 H12 H N N 160 PG5 H13 H N N 161 PG5 H21 H N N 162 PG5 H22 H N N 163 PG5 H31 H N N 164 PG5 H32 H N N 165 PG5 H41 H N N 166 PG5 H42 H N N 167 PG5 H51 H N N 168 PG5 H52 H N N 169 PG5 H61 H N N 170 PG5 H62 H N N 171 PG5 H71 H N N 172 PG5 H72 H N N 173 PG5 H81 H N N 174 PG5 H82 H N N 175 PG5 H83 H N N 176 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 PG5 C1 O1 sing N N 152 PG5 C1 H11 sing N N 153 PG5 C1 H12 sing N N 154 PG5 C1 H13 sing N N 155 PG5 O1 C2 sing N N 156 PG5 C2 C3 sing N N 157 PG5 C2 H21 sing N N 158 PG5 C2 H22 sing N N 159 PG5 C3 O2 sing N N 160 PG5 C3 H31 sing N N 161 PG5 C3 H32 sing N N 162 PG5 O2 C4 sing N N 163 PG5 C4 C5 sing N N 164 PG5 C4 H41 sing N N 165 PG5 C4 H42 sing N N 166 PG5 C5 O3 sing N N 167 PG5 C5 H51 sing N N 168 PG5 C5 H52 sing N N 169 PG5 O3 C6 sing N N 170 PG5 C6 C7 sing N N 171 PG5 C6 H61 sing N N 172 PG5 C6 H62 sing N N 173 PG5 C7 O4 sing N N 174 PG5 C7 H71 sing N N 175 PG5 C7 H72 sing N N 176 PG5 O4 C8 sing N N 177 PG5 C8 H81 sing N N 178 PG5 C8 H82 sing N N 179 PG5 C8 H83 sing N N 180 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8DHC 'double helix' 8DHC 'z-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 15 1_555 -0.643 3.513 0.257 3.439 -10.421 -79.982 1 A_DC1:DG15_B A 1 ? B 15 ? ? ? 1 B DG 19 1_555 A DG 6 1_555 3.523 7.998 0.353 -10.079 36.479 178.758 2 B_DG19:DG6_A B 19 ? A 6 ? 4 12 1 A DC 5 1_555 B DC 18 1_555 -1.964 -1.221 -0.421 -5.579 -2.859 -176.194 3 A_DC5:DC18_B A 5 ? B 18 ? 15 2 1 A DC 9 1_555 B DC 23 1_555 -1.998 -1.701 0.097 -2.676 -2.101 -177.651 4 A_DC9:DC23_B A 9 ? B 23 ? 15 2 1 A DC 4 1_555 B DC 17 1_555 -1.883 -1.439 0.368 10.197 -0.517 -179.108 5 A_DC4:DC17_B A 4 ? B 17 ? 15 2 1 A DC 10 1_555 B DC 24 1_555 2.027 1.469 0.192 5.626 5.740 179.599 6 A_DC10:DC24_B A 10 ? B 24 ? 15 2 1 A DC 3 1_555 B DC 16 1_555 -1.851 -1.435 -0.278 13.261 -13.223 -178.893 7 A_DC3:DC16_B A 3 ? B 16 ? 15 2 1 A DC 11 1_555 B DC 25 1_555 -1.822 -1.318 0.037 -4.129 3.374 -178.237 8 A_DC11:DC25_B A 11 ? B 25 ? 15 2 1 A DG 2 1_555 B DC 14 1_555 -0.133 -0.282 -0.003 0.287 21.324 0.624 9 A_DG2:DC14_B A 2 ? B 14 ? 19 1 1 B DG 13 1_555 A DG 13 1_555 3.457 -8.442 0.073 7.058 4.574 174.359 10 B_DG13:DG13_A B 13 ? A 13 ? 4 12 1 A DT 12 1_555 B DT 12 1_555 1.758 -3.156 -0.092 28.584 15.759 178.965 11 A_DT12:DT12_B A 12 ? B 12 ? 13 2 1 A DG 15 1_555 B DC 1 1_555 0.153 -3.741 -0.275 0.752 15.927 73.958 12 A_DG15:DC1_B A 15 ? B 1 ? ? ? 1 B DG 6 1_555 A DG 19 1_555 3.400 7.805 -0.687 -8.677 38.071 179.504 13 B_DG6:DG19_A B 6 ? A 19 ? 4 12 1 A DC 18 1_555 B DC 5 1_555 2.003 1.419 0.668 5.134 0.755 179.712 14 A_DC18:DC5_B A 18 ? B 5 ? 15 2 1 A DC 23 1_555 B DC 9 1_555 2.128 1.855 0.032 1.338 2.874 178.901 15 A_DC23:DC9_B A 23 ? B 9 ? 15 2 1 A DC 17 1_555 B DC 4 1_555 2.007 1.270 -0.089 -12.096 -7.881 179.102 16 A_DC17:DC4_B A 17 ? B 4 ? 15 2 1 A DC 24 1_555 B DC 10 1_555 -2.026 -1.671 -0.113 -3.538 -6.984 -176.173 17 A_DC24:DC10_B A 24 ? B 10 ? 15 2 1 A DC 16 1_555 B DC 3 1_555 -1.833 -0.901 0.597 10.978 -7.443 -177.787 18 A_DC16:DC3_B A 16 ? B 3 ? 15 2 1 A DC 25 1_555 B DC 11 1_555 1.607 0.945 -0.070 6.207 -4.374 176.149 19 A_DC25:DC11_B A 25 ? B 11 ? 15 2 1 A DC 14 1_555 B DG 2 1_555 0.134 -0.238 0.114 0.525 19.157 -4.501 20 A_DC14:DG2_B A 14 ? B 2 ? 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 B DG 19 1_555 A DG 6 1_555 A DC 5 1_555 B DC 18 1_555 -0.015 -0.201 -2.865 -0.635 -2.538 -56.355 0.087 0.016 -2.871 2.686 -0.672 -56.411 1 BA_DG19DC5:DC18DG6_BA B 19 ? A 6 ? A 5 ? B 18 ? 1 A DC 5 1_555 B DC 18 1_555 A DC 9 1_555 B DC 23 1_555 -1.812 2.339 0.398 -144.931 -97.692 34.443 1.315 0.692 0.304 -49.872 73.988 175.016 2 AA_DC5DC9:DC23DC18_BB A 5 ? B 18 ? A 9 ? B 23 ? 1 A DC 9 1_555 B DC 23 1_555 A DC 4 1_555 B DC 17 1_555 2.096 -2.522 0.231 -134.424 -110.989 -161.024 1.273 1.033 0.229 55.519 -67.242 -179.065 3 AA_DC9DC4:DC17DC23_BB A 9 ? B 23 ? A 4 ? B 17 ? 1 A DC 4 1_555 B DC 17 1_555 A DC 10 1_555 B DC 24 1_555 2.388 1.644 0.043 -93.405 147.527 -24.500 -0.804 1.208 -0.100 -75.557 -47.838 -174.733 4 AA_DC4DC10:DC24DC17_BB A 4 ? B 17 ? A 10 ? B 24 ? 1 A DC 10 1_555 B DC 24 1_555 A DC 3 1_555 B DC 16 1_555 2.793 2.389 -0.119 116.433 -133.717 -130.445 -1.215 1.379 -0.122 66.952 58.298 -178.870 5 AA_DC10DC3:DC16DC24_BB A 10 ? B 24 ? A 3 ? B 16 ? 1 A DC 3 1_555 B DC 16 1_555 A DC 11 1_555 B DC 25 1_555 0.981 -2.787 -0.499 152.433 89.369 -27.032 1.408 0.468 0.432 -45.324 77.308 -176.791 6 AA_DC3DC11:DC25DC16_BB A 3 ? B 16 ? A 11 ? B 25 ? 1 A DC 11 1_555 B DC 25 1_555 A DG 2 1_555 B DC 14 1_555 5.800 1.470 2.812 -12.397 -86.892 -10.679 2.325 3.681 2.630 83.627 -11.931 -88.288 7 AA_DC11DG2:DC14DC25_BB A 11 ? B 25 ? A 2 ? B 14 ? 1 B DG 13 1_555 A DG 13 1_555 A DT 12 1_555 B DT 12 1_555 -0.159 0.201 3.213 -1.024 0.214 -111.714 -0.124 -0.108 3.211 -0.129 -0.619 -111.717 8 BA_DG13DT12:DT12DG13_BA B 13 ? A 13 ? A 12 ? B 12 ? 1 B DG 6 1_555 A DG 19 1_555 A DC 18 1_555 B DC 5 1_555 -0.023 -0.197 -2.769 1.548 -0.580 125.649 -0.115 0.002 -2.769 -0.326 -0.870 125.656 9 BA_DG6DC18:DC5DG19_BA B 6 ? A 19 ? A 18 ? B 5 ? 1 A DC 18 1_555 B DC 5 1_555 A DC 23 1_555 B DC 9 1_555 -1.613 2.613 0.479 -145.983 -98.054 126.234 1.363 0.722 0.374 -49.152 73.177 178.127 10 AA_DC18DC23:DC9DC5_BB A 18 ? B 5 ? A 23 ? B 9 ? 1 A DC 23 1_555 B DC 9 1_555 A DC 17 1_555 B DC 4 1_555 2.042 -2.196 0.020 -134.983 -112.109 -75.952 1.124 0.991 0.144 56.611 -68.162 -176.427 11 AA_DC23DC17:DC4DC9_BB A 23 ? B 9 ? A 17 ? B 4 ? 1 A DC 17 1_555 B DC 4 1_555 A DC 24 1_555 B DC 10 1_555 2.757 1.567 -0.221 -96.760 149.862 176.135 0.787 -1.377 -0.227 74.931 48.380 179.946 12 AA_DC17DC24:DC10DC4_BB A 17 ? B 4 ? A 24 ? B 10 ? 1 A DC 24 1_555 B DC 10 1_555 A DC 16 1_555 B DC 3 1_555 2.340 -2.526 0.432 -126.673 -117.176 -53.065 1.397 1.030 0.196 59.985 -64.847 -173.343 13 AA_DC24DC16:DC3DC10_BB A 24 ? B 10 ? A 16 ? B 3 ? 1 A DC 16 1_555 B DC 3 1_555 A DC 25 1_555 B DC 11 1_555 3.092 1.022 0.481 -97.032 147.398 52.562 0.528 -1.536 -0.546 74.520 49.057 176.834 14 AA_DC16DC25:DC11DC3_BB A 16 ? B 3 ? A 25 ? B 11 ? 1 A DC 25 1_555 B DC 11 1_555 A DC 14 1_555 B DG 2 1_555 2.688 2.342 5.409 88.806 -6.438 165.891 1.193 -1.110 5.606 -3.234 -44.620 169.952 15 AA_DC25DC14:DG2DC11_BB A 25 ? B 11 ? A 14 ? B 2 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Cancer Institute (NIH/NCI)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 1R15CA253134 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE' PG5 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 8CXF _pdbx_initial_refinement_model.details ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'native gel electrophoresis' _pdbx_struct_assembly_auth_evidence.details 'There are bands for both monomer and a dimer on the native gel.' # _space_group.name_H-M_alt 'C 1 2 1' _space_group.name_Hall 'C 2y' _space_group.IT_number 5 _space_group.crystal_system monoclinic _space_group.id 1 #