data_6WY3 # _entry.id 6WY3 # _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 6WY3 pdb_00006wy3 10.2210/pdb6wy3/pdb WWPDB D_1000240689 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6WY3 _pdbx_database_status.recvd_initial_deposition_date 2020-05-12 _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 'Sekula, B.' 1 ? 'Ruszkowski, M.' 2 ? 'Mao, S.' 3 ? 'Haruehanroengra, P.' 4 ? 'Sheng, J.' 5 ? # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 48 _citation.language ? _citation.page_first 10087 _citation.page_last 10100 _citation.title 'Base pairing, structural and functional insights into N4-methylcytidine (m4C) and N4,N4-dimethylcytidine (m42C) modified RNA.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkaa737 _citation.pdbx_database_id_PubMed 32941619 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mao, S.' 1 ? primary 'Sekula, B.' 2 ? primary 'Ruszkowski, M.' 3 ? primary 'Ranganathan, S.V.' 4 ? primary 'Haruehanroengra, P.' 5 ? primary 'Wu, Y.' 6 ? primary 'Shen, F.' 7 ? primary 'Sheng, J.' 8 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 6WY3 _cell.details ? _cell.formula_units_Z ? _cell.length_a 33.086 _cell.length_a_esd ? _cell.length_b 36.184 _cell.length_b_esd ? _cell.length_c 105.050 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 16 _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 ? # _symmetry.entry_id 6WY3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _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 ;RNA (5'-R(*CP*CP*GP*GP*(LV2)P*GP*CP*CP*GP*G)-3') ; 3235.033 4 ? ? ? ? 2 water nat water 18.015 187 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'CCGG(LV2)GCCGG' _entity_poly.pdbx_seq_one_letter_code_can CCGGCGCCGG _entity_poly.pdbx_strand_id A,B,C,D _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 C n 1 2 C n 1 3 G n 1 4 G n 1 5 LV2 n 1 6 G n 1 7 C n 1 8 C n 1 9 G n 1 10 G 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 10 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6WY3 _struct_ref.pdbx_db_accession 6WY3 _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 6WY3 A 1 ? 10 ? 6WY3 1 ? 10 ? 1 10 2 1 6WY3 B 1 ? 10 ? 6WY3 1 ? 10 ? 1 10 3 1 6WY3 C 1 ? 10 ? 6WY3 1 ? 10 ? 1 10 4 1 6WY3 D 1 ? 10 ? 6WY3 1 ? 10 ? 1 10 # 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 LV2 'RNA linking' n ;[(2~{R},3~{S},4~{R},5~{R})-5-[4-(dimethylamino)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate ; ? 'C11 H18 N3 O8 P' 351.250 # _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 6WY3 _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 2.37 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 48.12 _exptl_crystal.description ? _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_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 7.0 _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 ;10% v/v (+/-)-2-Methyl-2,4-pentanediol (MPD), 0.040 M Sodium cacodylate trihydrate pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.08M Sodium chloride ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _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 EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-03-28 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Si (111)' _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 1.000 _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 22-ID' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.000 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 22-ID _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6WY3 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.647 _reflns.d_resolution_low 27.995 _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 14279 _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 -3 _reflns.percent_possible_obs 90.8 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.4 _reflns.pdbx_Rmerge_I_obs 0.096 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 6.7 _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 0.115 _reflns.pdbx_Rpim_I_all 0.061 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.993 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.647 _reflns_shell.d_res_low 1.687 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.4 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 709 _reflns_shell.percent_possible_all 80.4 _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 0.677 _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 3.1 _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 0.813 _reflns_shell.pdbx_Rpim_I_all 0.442 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.606 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? # _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 ? _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 6WY3 _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 1.647 _refine.ls_d_res_low 27.995 _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 14277 _refine.ls_number_reflns_R_free 692 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 89.55 _refine.ls_percent_reflns_R_free 4.85 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1908 _refine.ls_R_factor_R_free 0.2142 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1896 _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 ? _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 1.34 _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 4MS9 _refine.pdbx_stereochemistry_target_values ? _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 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 24.06 _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 0.12 _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.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 856 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 187 _refine_hist.number_atoms_total 1043 _refine_hist.d_res_high 1.647 _refine_hist.d_res_low 27.995 # 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' ? 0.006 ? 952 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.158 ? 1480 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 9.551 ? 468 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.042 ? 192 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.006 ? 44 ? f_plane_restr ? ? # 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' 1.6465 1.7736 . . 104 2106 71.00 . . . 0.2556 . 0.2232 . . . . . . . . . . . 'X-RAY DIFFRACTION' 1.7736 1.9520 . . 146 2766 93.00 . . . 0.2410 . 0.2147 . . . . . . . . . . . 'X-RAY DIFFRACTION' 1.9520 2.2344 . . 144 2942 98.00 . . . 0.2456 . 0.2137 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.2344 2.8147 . . 147 2803 93.00 . . . 0.2354 . 0.2228 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.8147 27.9990 . . 151 2968 93.00 . . . 0.1893 . 0.1622 . . . . . . . . . . . # _struct.entry_id 6WY3 _struct.title 'Crystal structure of RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG; P212121 form' _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 6WY3 _struct_keywords.text 'RNA DUPLEX, RNA' _struct_keywords.pdbx_keywords RNA # 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 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? # 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 G 4 "O3'" ? ? ? 1_555 A LV2 5 P ? ? A G 4 A LV2 5 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale2 covale one ? A LV2 5 "O3'" ? ? ? 1_555 A G 6 P ? ? A LV2 5 A G 6 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale3 covale both ? B G 4 "O3'" ? ? ? 1_555 B LV2 5 P ? ? B G 4 B LV2 5 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale4 covale one ? B LV2 5 "O3'" ? ? ? 1_555 B G 6 P ? ? B LV2 5 B G 6 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale5 covale both ? C G 4 "O3'" ? ? ? 1_555 C LV2 5 P ? ? C G 4 C LV2 5 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale6 covale one ? C LV2 5 "O3'" ? ? ? 1_555 C G 6 P ? ? C LV2 5 C G 6 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale7 covale both ? D G 4 "O3'" ? ? ? 1_555 D LV2 5 P ? ? D G 4 D LV2 5 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale8 covale one ? D LV2 5 "O3'" ? ? ? 1_555 D G 6 P ? ? D LV2 5 D G 6 1_555 ? ? ? ? ? ? ? 1.591 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 1 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 1 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 1 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 2 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 2 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 2 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 3 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 3 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 3 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 4 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 4 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 4 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A LV2 5 O2 ? ? ? 1_555 B G 6 N1 ? ? A LV2 5 B G 6 1_555 ? ? ? ? ? ? 'LV2-G MISPAIR' ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 B LV2 5 O2 ? ? A G 6 B LV2 5 1_555 ? ? ? ? ? ? 'G-LV2 MISPAIR' ? ? ? hydrog15 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 7 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 7 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 7 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 8 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 8 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 8 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 9 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 9 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 9 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 10 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 10 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 10 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C C 1 N3 ? ? ? 1_555 D G 10 N1 ? ? C C 1 D G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C C 1 N4 ? ? ? 1_555 D G 10 O6 ? ? C C 1 D G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C C 1 O2 ? ? ? 1_555 D G 10 N2 ? ? C C 1 D G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C C 2 N3 ? ? ? 1_555 D G 9 N1 ? ? C C 2 D G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C C 2 N4 ? ? ? 1_555 D G 9 O6 ? ? C C 2 D G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C C 2 O2 ? ? ? 1_555 D G 9 N2 ? ? C C 2 D G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C G 3 N1 ? ? ? 1_555 D C 8 N3 ? ? C G 3 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C G 3 N2 ? ? ? 1_555 D C 8 O2 ? ? C G 3 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C G 3 O6 ? ? ? 1_555 D C 8 N4 ? ? C G 3 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 7 N3 ? ? C G 4 D C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C G 4 N2 ? ? ? 1_555 D C 7 O2 ? ? C G 4 D C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C G 4 O6 ? ? ? 1_555 D C 7 N4 ? ? C G 4 D C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C LV2 5 O2 ? ? ? 1_555 D G 6 N1 ? ? C LV2 5 D G 6 1_555 ? ? ? ? ? ? 'LV2-G MISPAIR' ? ? ? hydrog40 hydrog ? ? C G 6 N1 ? ? ? 1_555 D LV2 5 O2 ? ? C G 6 D LV2 5 1_555 ? ? ? ? ? ? 'G-LV2 MISPAIR' ? ? ? hydrog41 hydrog ? ? C C 7 N3 ? ? ? 1_555 D G 4 N1 ? ? C C 7 D G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C C 7 N4 ? ? ? 1_555 D G 4 O6 ? ? C C 7 D G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C C 7 O2 ? ? ? 1_555 D G 4 N2 ? ? C C 7 D G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C C 8 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 8 D G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C C 8 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 8 D G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C C 8 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 8 D G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C G 9 N1 ? ? ? 1_555 D C 2 N3 ? ? C G 9 D C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C G 9 N2 ? ? ? 1_555 D C 2 O2 ? ? C G 9 D C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C G 9 O6 ? ? ? 1_555 D C 2 N4 ? ? C G 9 D C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C G 10 N1 ? ? ? 1_555 D C 1 N3 ? ? C G 10 D C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C G 10 N2 ? ? ? 1_555 D C 1 O2 ? ? C G 10 D C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C G 10 O6 ? ? ? 1_555 D C 1 N4 ? ? C G 10 D C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 6WY3 _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] 0.030224 _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] 0.027637 _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] 0.009519 _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 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 C 1 1 1 C C A . n A 1 2 C 2 2 2 C C A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 LV2 5 5 5 LV2 cn2 A . n A 1 6 G 6 6 6 G G A . n A 1 7 C 7 7 7 C C A . n A 1 8 C 8 8 8 C C A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n B 1 1 C 1 1 1 C C B . n B 1 2 C 2 2 2 C C B . n B 1 3 G 3 3 3 G G B . n B 1 4 G 4 4 4 G G B . n B 1 5 LV2 5 5 5 LV2 cn2 B . n B 1 6 G 6 6 6 G G B . n B 1 7 C 7 7 7 C C B . n B 1 8 C 8 8 8 C C B . n B 1 9 G 9 9 9 G G B . n B 1 10 G 10 10 10 G G B . n C 1 1 C 1 1 1 C C C . n C 1 2 C 2 2 2 C C C . n C 1 3 G 3 3 3 G G C . n C 1 4 G 4 4 4 G G C . n C 1 5 LV2 5 5 5 LV2 cn2 C . n C 1 6 G 6 6 6 G G C . n C 1 7 C 7 7 7 C C C . n C 1 8 C 8 8 8 C C C . n C 1 9 G 9 9 9 G G C . n C 1 10 G 10 10 10 G G C . n D 1 1 C 1 1 1 C C D . n D 1 2 C 2 2 2 C C D . n D 1 3 G 3 3 3 G G D . n D 1 4 G 4 4 4 G G D . n D 1 5 LV2 5 5 5 LV2 cn2 D . n D 1 6 G 6 6 6 G G D . n D 1 7 C 7 7 7 C C D . n D 1 8 C 8 8 8 C C D . n D 1 9 G 9 9 9 G G D . n D 1 10 G 10 10 10 G G D . 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 E 2 HOH 1 101 166 HOH HOH A . E 2 HOH 2 102 189 HOH HOH A . E 2 HOH 3 103 94 HOH HOH A . E 2 HOH 4 104 173 HOH HOH A . E 2 HOH 5 105 95 HOH HOH A . E 2 HOH 6 106 167 HOH HOH A . E 2 HOH 7 107 128 HOH HOH A . E 2 HOH 8 108 89 HOH HOH A . E 2 HOH 9 109 169 HOH HOH A . E 2 HOH 10 110 131 HOH HOH A . E 2 HOH 11 111 140 HOH HOH A . E 2 HOH 12 112 104 HOH HOH A . E 2 HOH 13 113 85 HOH HOH A . E 2 HOH 14 114 181 HOH HOH A . E 2 HOH 15 115 162 HOH HOH A . E 2 HOH 16 116 88 HOH HOH A . E 2 HOH 17 117 83 HOH HOH A . E 2 HOH 18 118 101 HOH HOH A . E 2 HOH 19 119 117 HOH HOH A . E 2 HOH 20 120 161 HOH HOH A . E 2 HOH 21 121 147 HOH HOH A . E 2 HOH 22 122 139 HOH HOH A . E 2 HOH 23 123 126 HOH HOH A . E 2 HOH 24 124 81 HOH HOH A . E 2 HOH 25 125 100 HOH HOH A . E 2 HOH 26 126 80 HOH HOH A . E 2 HOH 27 127 110 HOH HOH A . E 2 HOH 28 128 127 HOH HOH A . E 2 HOH 29 129 154 HOH HOH A . E 2 HOH 30 130 116 HOH HOH A . E 2 HOH 31 131 109 HOH HOH A . E 2 HOH 32 132 92 HOH HOH A . E 2 HOH 33 133 192 HOH HOH A . E 2 HOH 34 134 134 HOH HOH A . E 2 HOH 35 135 148 HOH HOH A . E 2 HOH 36 136 87 HOH HOH A . E 2 HOH 37 137 82 HOH HOH A . E 2 HOH 38 138 113 HOH HOH A . E 2 HOH 39 139 160 HOH HOH A . E 2 HOH 40 140 115 HOH HOH A . E 2 HOH 41 141 155 HOH HOH A . E 2 HOH 42 142 78 HOH HOH A . E 2 HOH 43 143 137 HOH HOH A . E 2 HOH 44 144 198 HOH HOH A . E 2 HOH 45 145 102 HOH HOH A . E 2 HOH 46 146 196 HOH HOH A . E 2 HOH 47 147 150 HOH HOH A . E 2 HOH 48 148 183 HOH HOH A . E 2 HOH 49 149 112 HOH HOH A . E 2 HOH 50 150 165 HOH HOH A . F 2 HOH 1 101 125 HOH HOH B . F 2 HOH 2 102 132 HOH HOH B . F 2 HOH 3 103 79 HOH HOH B . F 2 HOH 4 104 105 HOH HOH B . F 2 HOH 5 105 152 HOH HOH B . F 2 HOH 6 106 97 HOH HOH B . F 2 HOH 7 107 107 HOH HOH B . F 2 HOH 8 108 164 HOH HOH B . F 2 HOH 9 109 141 HOH HOH B . F 2 HOH 10 110 122 HOH HOH B . F 2 HOH 11 111 86 HOH HOH B . F 2 HOH 12 112 197 HOH HOH B . F 2 HOH 13 113 138 HOH HOH B . F 2 HOH 14 114 156 HOH HOH B . F 2 HOH 15 115 106 HOH HOH B . F 2 HOH 16 116 90 HOH HOH B . F 2 HOH 17 117 142 HOH HOH B . F 2 HOH 18 118 98 HOH HOH B . F 2 HOH 19 119 145 HOH HOH B . F 2 HOH 20 120 144 HOH HOH B . F 2 HOH 21 121 91 HOH HOH B . F 2 HOH 22 122 103 HOH HOH B . F 2 HOH 23 123 118 HOH HOH B . F 2 HOH 24 124 133 HOH HOH B . F 2 HOH 25 125 143 HOH HOH B . F 2 HOH 26 126 96 HOH HOH B . F 2 HOH 27 127 120 HOH HOH B . F 2 HOH 28 128 121 HOH HOH B . F 2 HOH 29 129 168 HOH HOH B . F 2 HOH 30 130 170 HOH HOH B . F 2 HOH 31 131 119 HOH HOH B . F 2 HOH 32 132 157 HOH HOH B . F 2 HOH 33 133 159 HOH HOH B . F 2 HOH 34 134 151 HOH HOH B . F 2 HOH 35 135 135 HOH HOH B . F 2 HOH 36 136 184 HOH HOH B . F 2 HOH 37 137 136 HOH HOH B . F 2 HOH 38 138 129 HOH HOH B . F 2 HOH 39 139 99 HOH HOH B . F 2 HOH 40 140 108 HOH HOH B . F 2 HOH 41 141 84 HOH HOH B . F 2 HOH 42 142 202 HOH HOH B . F 2 HOH 43 143 171 HOH HOH B . F 2 HOH 44 144 153 HOH HOH B . F 2 HOH 45 145 149 HOH HOH B . F 2 HOH 46 146 111 HOH HOH B . F 2 HOH 47 147 114 HOH HOH B . F 2 HOH 48 148 188 HOH HOH B . G 2 HOH 1 101 56 HOH HOH C . G 2 HOH 2 102 61 HOH HOH C . G 2 HOH 3 103 65 HOH HOH C . G 2 HOH 4 104 59 HOH HOH C . G 2 HOH 5 105 27 HOH HOH C . G 2 HOH 6 106 48 HOH HOH C . G 2 HOH 7 107 55 HOH HOH C . G 2 HOH 8 108 35 HOH HOH C . G 2 HOH 9 109 28 HOH HOH C . G 2 HOH 10 110 3 HOH HOH C . G 2 HOH 11 111 74 HOH HOH C . G 2 HOH 12 112 70 HOH HOH C . G 2 HOH 13 113 17 HOH HOH C . G 2 HOH 14 114 16 HOH HOH C . G 2 HOH 15 115 53 HOH HOH C . G 2 HOH 16 116 177 HOH HOH C . G 2 HOH 17 117 67 HOH HOH C . G 2 HOH 18 118 76 HOH HOH C . G 2 HOH 19 119 47 HOH HOH C . G 2 HOH 20 120 63 HOH HOH C . G 2 HOH 21 121 12 HOH HOH C . G 2 HOH 22 122 195 HOH HOH C . G 2 HOH 23 123 193 HOH HOH C . G 2 HOH 24 124 18 HOH HOH C . G 2 HOH 25 125 40 HOH HOH C . G 2 HOH 26 126 179 HOH HOH C . G 2 HOH 27 127 34 HOH HOH C . G 2 HOH 28 128 208 HOH HOH C . G 2 HOH 29 129 23 HOH HOH C . G 2 HOH 30 130 49 HOH HOH C . G 2 HOH 31 131 26 HOH HOH C . G 2 HOH 32 132 163 HOH HOH C . G 2 HOH 33 133 14 HOH HOH C . G 2 HOH 34 134 7 HOH HOH C . G 2 HOH 35 135 51 HOH HOH C . G 2 HOH 36 136 24 HOH HOH C . G 2 HOH 37 137 72 HOH HOH C . G 2 HOH 38 138 19 HOH HOH C . G 2 HOH 39 139 73 HOH HOH C . G 2 HOH 40 140 57 HOH HOH C . G 2 HOH 41 141 15 HOH HOH C . G 2 HOH 42 142 60 HOH HOH C . G 2 HOH 43 143 66 HOH HOH C . G 2 HOH 44 144 68 HOH HOH C . G 2 HOH 45 145 30 HOH HOH C . G 2 HOH 46 146 9 HOH HOH C . G 2 HOH 47 147 180 HOH HOH C . G 2 HOH 48 148 75 HOH HOH C . G 2 HOH 49 149 209 HOH HOH C . G 2 HOH 50 150 37 HOH HOH C . H 2 HOH 1 101 13 HOH HOH D . H 2 HOH 2 102 32 HOH HOH D . H 2 HOH 3 103 31 HOH HOH D . H 2 HOH 4 104 50 HOH HOH D . H 2 HOH 5 105 93 HOH HOH D . H 2 HOH 6 106 41 HOH HOH D . H 2 HOH 7 107 4 HOH HOH D . H 2 HOH 8 108 21 HOH HOH D . H 2 HOH 9 109 175 HOH HOH D . H 2 HOH 10 110 172 HOH HOH D . H 2 HOH 11 111 6 HOH HOH D . H 2 HOH 12 112 11 HOH HOH D . H 2 HOH 13 113 124 HOH HOH D . H 2 HOH 14 114 5 HOH HOH D . H 2 HOH 15 115 54 HOH HOH D . H 2 HOH 16 116 29 HOH HOH D . H 2 HOH 17 117 58 HOH HOH D . H 2 HOH 18 118 77 HOH HOH D . H 2 HOH 19 119 38 HOH HOH D . H 2 HOH 20 120 25 HOH HOH D . H 2 HOH 21 121 64 HOH HOH D . H 2 HOH 22 122 36 HOH HOH D . H 2 HOH 23 123 2 HOH HOH D . H 2 HOH 24 124 44 HOH HOH D . H 2 HOH 25 125 20 HOH HOH D . H 2 HOH 26 126 174 HOH HOH D . H 2 HOH 27 127 62 HOH HOH D . H 2 HOH 28 128 52 HOH HOH D . H 2 HOH 29 129 39 HOH HOH D . H 2 HOH 30 130 207 HOH HOH D . H 2 HOH 31 131 45 HOH HOH D . H 2 HOH 32 132 10 HOH HOH D . H 2 HOH 33 133 33 HOH HOH D . H 2 HOH 34 134 8 HOH HOH D . H 2 HOH 35 135 69 HOH HOH D . H 2 HOH 36 136 71 HOH HOH D . H 2 HOH 37 137 43 HOH HOH D . H 2 HOH 38 138 210 HOH HOH D . H 2 HOH 39 139 22 HOH HOH D . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F 2 1 C,D,G,H # 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)' 1120 ? 1 MORE -2 ? 1 'SSA (A^2)' 3830 ? 2 'ABSA (A^2)' 1120 ? 2 MORE -3 ? 2 'SSA (A^2)' 3840 ? # _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 2020-09-02 2 'Structure model' 1 1 2021-03-17 3 'Structure model' 1 2 2023-10-18 # _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' 'Database references' 4 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 2 'Structure model' citation_author 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' database_2 6 3 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.journal_volume' 7 2 'Structure model' '_citation.page_first' 8 2 'Structure model' '_citation.page_last' 9 2 'Structure model' '_citation.pdbx_database_id_DOI' 10 2 'Structure model' '_citation.pdbx_database_id_PubMed' 11 2 'Structure model' '_citation.title' 12 2 'Structure model' '_citation.year' 13 3 'Structure model' '_database_2.pdbx_DOI' 14 3 'Structure model' '_database_2.pdbx_database_accession' # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined 5.1403 18.5122 50.7379 0.2856 ? 0.0048 ? 0.0108 ? 0.1803 ? 0.0054 ? 0.1798 ? 3.0886 ? -1.0618 ? -2.0477 ? 0.3893 ? 0.8825 ? 0.8517 ? 0.0508 ? -0.1549 ? 0.1528 ? 0.0534 ? 0.0706 ? 0.0376 ? -0.0530 ? 0.0862 ? -0.1307 ? 2 'X-RAY DIFFRACTION' ? refined 4.9602 18.2295 46.1783 0.2203 ? -0.0136 ? -0.0103 ? 0.1765 ? 0.0001 ? 0.1292 ? 2.9348 ? -0.7190 ? -1.8061 ? 2.2812 ? 0.1417 ? 1.0291 ? -0.0021 ? 0.2733 ? 0.0927 ? -0.0959 ? 0.0422 ? -0.1065 ? 0.1453 ? -0.1118 ? -0.0821 ? 3 'X-RAY DIFFRACTION' ? refined 7.7057 17.1413 23.5437 0.2230 ? -0.0276 ? -0.0102 ? 0.2583 ? -0.0224 ? 0.1670 ? 0.4398 ? 0.9406 ? -1.6451 ? 2.3649 ? -2.9190 ? 1.7234 ? 0.1532 ? -0.1082 ? 0.0301 ? 0.1808 ? 0.0559 ? 0.2271 ? -0.0489 ? 0.0422 ? -0.1961 ? 4 'X-RAY DIFFRACTION' ? refined 7.8540 15.6729 19.6610 0.2410 ? 0.0347 ? -0.0149 ? 0.1994 ? -0.0476 ? 0.1200 ? 1.3522 ? -0.3103 ? 0.4966 ? 3.1406 ? -3.8810 ? 3.1197 ? 0.1291 ? 0.0724 ? 0.0230 ? -0.3498 ? 0.0035 ? 0.1188 ? 0.2745 ? 0.0785 ? -0.0949 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_PDB_ins_code _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 ? ? ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 1 through 10 ) ; 2 'X-RAY DIFFRACTION' 2 ? ? ? ? ? ? ? ? ? ? ? ;chain 'B' and (resid 1 through 10 ) ; 3 'X-RAY DIFFRACTION' 3 ? ? ? ? ? ? ? ? ? ? ? ;chain 'C' and (resid 1 through 10 ) ; 4 'X-RAY DIFFRACTION' 4 ? ? ? ? ? ? ? ? ? ? ? ;chain 'D' and (resid 1 through 10 ) ; # 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 ? ? ? '(1.11.1_2575)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? STARANISO ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _pdbx_entry_details.entry_id 6WY3 _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 G OP3 O N N 36 G P P N N 37 G OP1 O N N 38 G OP2 O N N 39 G "O5'" O N N 40 G "C5'" C N N 41 G "C4'" C N R 42 G "O4'" O N N 43 G "C3'" C N S 44 G "O3'" O N N 45 G "C2'" C N R 46 G "O2'" O N N 47 G "C1'" C N R 48 G N9 N Y N 49 G C8 C Y N 50 G N7 N Y N 51 G C5 C Y N 52 G C6 C N N 53 G O6 O N N 54 G N1 N N N 55 G C2 C N N 56 G N2 N N N 57 G N3 N N N 58 G C4 C Y N 59 G HOP3 H N N 60 G HOP2 H N N 61 G "H5'" H N N 62 G "H5''" H N N 63 G "H4'" H N N 64 G "H3'" H N N 65 G "HO3'" H N N 66 G "H2'" H N N 67 G "HO2'" H N N 68 G "H1'" H N N 69 G H8 H N N 70 G H1 H N N 71 G H21 H N N 72 G H22 H N N 73 HOH O O N N 74 HOH H1 H N N 75 HOH H2 H N N 76 LV2 P P N N 77 LV2 OP1 O N N 78 LV2 OP2 O N N 79 LV2 "O5'" O N N 80 LV2 "C5'" C N N 81 LV2 "C4'" C N R 82 LV2 "O4'" O N N 83 LV2 "C3'" C N S 84 LV2 "C2'" C N R 85 LV2 "O2'" O N N 86 LV2 "C1'" C N R 87 LV2 N1 N N N 88 LV2 C2 C N N 89 LV2 O2 O N N 90 LV2 N3 N N N 91 LV2 C4 C N N 92 LV2 N4 N N N 93 LV2 C5 C N N 94 LV2 C6 C N N 95 LV2 CM4 C N N 96 LV2 "O3'" O N N 97 LV2 C1 C N N 98 LV2 H2 H N N 99 LV2 H3 H N N 100 LV2 H4 H N N 101 LV2 H5 H N N 102 LV2 H6 H N N 103 LV2 H7 H N N 104 LV2 H8 H N N 105 LV2 H9 H N N 106 LV2 H10 H N N 107 LV2 H11 H N N 108 LV2 H12 H N N 109 LV2 H13 H N N 110 LV2 H14 H N N 111 LV2 H15 H N N 112 LV2 H16 H N N 113 LV2 H17 H N N 114 LV2 H18 H N N 115 LV2 OP3 O N N 116 LV2 H1 H N N 117 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 G OP3 P sing N N 37 G OP3 HOP3 sing N N 38 G P OP1 doub N N 39 G P OP2 sing N N 40 G P "O5'" sing N N 41 G OP2 HOP2 sing N N 42 G "O5'" "C5'" sing N N 43 G "C5'" "C4'" sing N N 44 G "C5'" "H5'" sing N N 45 G "C5'" "H5''" sing N N 46 G "C4'" "O4'" sing N N 47 G "C4'" "C3'" sing N N 48 G "C4'" "H4'" sing N N 49 G "O4'" "C1'" sing N N 50 G "C3'" "O3'" sing N N 51 G "C3'" "C2'" sing N N 52 G "C3'" "H3'" sing N N 53 G "O3'" "HO3'" sing N N 54 G "C2'" "O2'" sing N N 55 G "C2'" "C1'" sing N N 56 G "C2'" "H2'" sing N N 57 G "O2'" "HO2'" sing N N 58 G "C1'" N9 sing N N 59 G "C1'" "H1'" sing N N 60 G N9 C8 sing Y N 61 G N9 C4 sing Y N 62 G C8 N7 doub Y N 63 G C8 H8 sing N N 64 G N7 C5 sing Y N 65 G C5 C6 sing N N 66 G C5 C4 doub Y N 67 G C6 O6 doub N N 68 G C6 N1 sing N N 69 G N1 C2 sing N N 70 G N1 H1 sing N N 71 G C2 N2 sing N N 72 G C2 N3 doub N N 73 G N2 H21 sing N N 74 G N2 H22 sing N N 75 G N3 C4 sing N N 76 HOH O H1 sing N N 77 HOH O H2 sing N N 78 LV2 OP1 P doub N N 79 LV2 "C5'" "C4'" sing N N 80 LV2 "C5'" "O5'" sing N N 81 LV2 P "O5'" sing N N 82 LV2 P OP2 sing N N 83 LV2 "O3'" "C3'" sing N N 84 LV2 "C4'" "C3'" sing N N 85 LV2 "C4'" "O4'" sing N N 86 LV2 "C3'" "C2'" sing N N 87 LV2 "O4'" "C1'" sing N N 88 LV2 "O2'" "C2'" sing N N 89 LV2 "C2'" "C1'" sing N N 90 LV2 "C1'" N1 sing N N 91 LV2 C6 N1 sing N N 92 LV2 C6 C5 doub N N 93 LV2 N1 C2 sing N N 94 LV2 C5 C4 sing N N 95 LV2 C2 O2 doub N N 96 LV2 C2 N3 sing N N 97 LV2 C4 N3 doub N N 98 LV2 C4 N4 sing N N 99 LV2 C1 N4 sing N N 100 LV2 N4 CM4 sing N N 101 LV2 OP2 H2 sing N N 102 LV2 "C5'" H3 sing N N 103 LV2 "C5'" H4 sing N N 104 LV2 "C4'" H5 sing N N 105 LV2 "C3'" H6 sing N N 106 LV2 "C2'" H7 sing N N 107 LV2 "O2'" H8 sing N N 108 LV2 "C1'" H9 sing N N 109 LV2 C5 H10 sing N N 110 LV2 C6 H11 sing N N 111 LV2 CM4 H12 sing N N 112 LV2 CM4 H13 sing N N 113 LV2 CM4 H14 sing N N 114 LV2 "O3'" H15 sing N N 115 LV2 C1 H16 sing N N 116 LV2 C1 H17 sing N N 117 LV2 C1 H18 sing N N 118 LV2 P OP3 sing N N 119 LV2 OP3 H1 sing N N 120 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6WY3 'double helix' 6WY3 'a-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 B C 1 1_555 A G 10 1_555 0.300 -0.149 -0.192 8.623 -12.508 0.106 1 B_C1:G10_A B 1 ? A 10 ? 19 1 1 B C 2 1_555 A G 9 1_555 0.111 -0.109 -0.142 6.766 -9.489 -0.701 2 B_C2:G9_A B 2 ? A 9 ? 19 1 1 B G 3 1_555 A C 8 1_555 -0.137 -0.146 -0.026 -1.539 -8.895 -0.329 3 B_G3:C8_A B 3 ? A 8 ? 19 1 1 B G 4 1_555 A C 7 1_555 -0.137 -0.154 -0.155 -11.587 -15.714 -0.464 4 B_G4:C7_A B 4 ? A 7 ? 19 1 1 B LV2 5 1_555 A G 6 1_555 2.755 -0.749 0.366 -6.382 -8.415 -1.779 5 B_LV25:G6_A B 5 ? A 6 ? ? ? 1 B G 6 1_555 A LV2 5 1_555 -2.716 -0.614 0.078 -3.463 -11.944 1.729 6 B_G6:LV25_A B 6 ? A 5 ? ? 1 1 B C 7 1_555 A G 4 1_555 0.187 -0.146 0.020 1.523 -11.612 0.209 7 B_C7:G4_A B 7 ? A 4 ? 19 1 1 B C 8 1_555 A G 3 1_555 0.077 -0.151 0.214 -0.492 -5.103 -3.200 8 B_C8:G3_A B 8 ? A 3 ? 19 1 1 B G 9 1_555 A C 2 1_555 -0.012 -0.176 -0.019 -4.308 -8.123 -0.108 9 B_G9:C2_A B 9 ? A 2 ? 19 1 1 B G 10 1_555 A C 1 1_555 -0.364 -0.106 -0.088 -9.349 -10.142 1.720 10 B_G10:C1_A B 10 ? A 1 ? 19 1 1 D C 1 1_555 C G 10 1_555 0.097 -0.140 0.066 0.541 -8.635 -1.895 11 D_C1:G10_C D 1 ? C 10 ? 19 1 1 D C 2 1_555 C G 9 1_555 0.107 -0.133 -0.036 8.015 -6.552 -0.539 12 D_C2:G9_C D 2 ? C 9 ? 19 1 1 D G 3 1_555 C C 8 1_555 -0.141 -0.176 -0.220 -2.386 -12.045 0.725 13 D_G3:C8_C D 3 ? C 8 ? 19 1 1 D G 4 1_555 C C 7 1_555 -0.004 -0.107 -0.098 -12.272 -12.474 -1.979 14 D_G4:C7_C D 4 ? C 7 ? 19 1 1 D LV2 5 1_555 C G 6 1_555 2.756 -0.668 0.316 -6.181 -3.727 -0.776 15 D_LV25:G6_C D 5 ? C 6 ? ? ? 1 D G 6 1_555 C LV2 5 1_555 -2.782 -0.705 -0.077 -1.558 -5.278 2.177 16 D_G6:LV25_C D 6 ? C 5 ? ? 1 1 D C 7 1_555 C G 4 1_555 0.126 -0.183 -0.127 4.008 -10.651 0.382 17 D_C7:G4_C D 7 ? C 4 ? 19 1 1 D C 8 1_555 C G 3 1_555 0.004 -0.109 -0.091 3.828 -5.793 -0.981 18 D_C8:G3_C D 8 ? C 3 ? 19 1 1 D G 9 1_555 C C 2 1_555 -0.065 -0.143 0.112 -1.385 -9.129 -2.379 19 D_G9:C2_C D 9 ? C 2 ? 19 1 1 D G 10 1_555 C C 1 1_555 -0.245 -0.140 -0.011 -5.365 -13.980 -1.248 20 D_G10:C1_C D 10 ? C 1 ? 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 C 1 1_555 A G 10 1_555 B C 2 1_555 A G 9 1_555 -0.394 -1.842 3.302 -1.655 11.269 30.169 -5.162 0.440 2.488 20.744 3.047 32.200 1 BB_C1C2:G9G10_AA B 1 ? A 10 ? B 2 ? A 9 ? 1 B C 2 1_555 A G 9 1_555 B G 3 1_555 A C 8 1_555 -0.035 -1.953 3.384 -1.211 11.019 29.038 -5.620 -0.152 2.494 21.033 2.312 31.039 2 BB_C2G3:C8G9_AA B 2 ? A 9 ? B 3 ? A 8 ? 1 B G 3 1_555 A C 8 1_555 B G 4 1_555 A C 7 1_555 0.217 -1.928 3.465 2.912 10.469 32.787 -4.836 0.075 2.747 17.942 -4.990 34.494 3 BB_G3G4:C7C8_AA B 3 ? A 8 ? B 4 ? A 7 ? 1 B G 4 1_555 A C 7 1_555 B LV2 5 1_555 A G 6 1_555 0.106 -1.167 3.126 -0.310 5.222 42.689 -2.075 -0.174 2.969 7.142 0.424 42.993 4 BB_G4LV25:G6C7_AA B 4 ? A 7 ? B 5 ? A 6 ? 1 B LV2 5 1_555 A G 6 1_555 B G 6 1_555 A LV2 5 1_555 0.893 -3.028 2.824 4.516 9.216 8.200 -18.475 -1.341 -0.049 46.224 -22.652 13.129 5 BB_LV25G6:LV25G6_AA B 5 ? A 6 ? B 6 ? A 5 ? 1 B G 6 1_555 A LV2 5 1_555 B C 7 1_555 A G 4 1_555 -0.447 -1.336 3.129 -1.299 0.818 44.141 -1.849 0.478 3.116 1.088 1.728 44.166 6 BB_G6C7:G4LV25_AA B 6 ? A 5 ? B 7 ? A 4 ? 1 B C 7 1_555 A G 4 1_555 B C 8 1_555 A G 3 1_555 -0.158 -1.640 3.300 -1.102 5.310 32.792 -3.731 0.097 3.008 9.326 1.936 33.225 7 BB_C7C8:G3G4_AA B 7 ? A 4 ? B 8 ? A 3 ? 1 B C 8 1_555 A G 3 1_555 B G 9 1_555 A C 2 1_555 0.712 -2.020 3.185 2.884 8.071 28.085 -5.553 -0.846 2.576 16.162 -5.775 29.338 8 BB_C8G9:C2G3_AA B 8 ? A 3 ? B 9 ? A 2 ? 1 B G 9 1_555 A C 2 1_555 B G 10 1_555 A C 1 1_555 0.468 -2.081 3.287 2.719 8.431 32.800 -4.827 -0.395 2.713 14.600 -4.709 33.944 9 BB_G9G10:C1C2_AA B 9 ? A 2 ? B 10 ? A 1 ? 1 B G 10 1_555 A C 1 1_555 D C 1 1_555 C G 10 1_555 -0.114 -2.600 3.112 -0.703 5.552 -10.500 4.120 -1.618 3.951 -27.887 -3.529 -11.894 10 BD_G10C1:G10C1_CA B 10 ? A 1 ? D 1 ? C 10 ? 1 D C 1 1_555 C G 10 1_555 D C 2 1_555 C G 9 1_555 0.169 -1.542 3.119 -0.130 8.085 29.886 -4.288 -0.340 2.621 15.327 0.247 30.936 11 DD_C1C2:G9G10_CC D 1 ? C 10 ? D 2 ? C 9 ? 1 D C 2 1_555 C G 9 1_555 D G 3 1_555 C C 8 1_555 0.318 -1.915 3.575 1.174 9.385 30.050 -5.300 -0.366 2.871 17.562 -2.197 31.471 12 DD_C2G3:C8G9_CC D 2 ? C 9 ? D 3 ? C 8 ? 1 D G 3 1_555 C C 8 1_555 D G 4 1_555 C C 7 1_555 0.007 -2.153 3.539 0.537 5.997 31.565 -4.991 0.085 3.088 10.901 -0.976 32.120 13 DD_G3G4:C7C8_CC D 3 ? C 8 ? D 4 ? C 7 ? 1 D G 4 1_555 C C 7 1_555 D LV2 5 1_555 C G 6 1_555 -0.169 -1.484 3.127 -0.576 3.809 40.289 -2.545 0.183 2.983 5.515 0.834 40.465 14 DD_G4LV25:G6C7_CC D 4 ? C 7 ? D 5 ? C 6 ? 1 D LV2 5 1_555 C G 6 1_555 D G 6 1_555 C LV2 5 1_555 1.087 -2.877 2.983 4.488 4.918 6.442 -25.681 0.442 1.077 33.971 -31.004 9.262 15 DD_LV25G6:LV25G6_CC D 5 ? C 6 ? D 6 ? C 5 ? 1 D G 6 1_555 C LV2 5 1_555 D C 7 1_555 C G 4 1_555 -0.240 -1.612 3.167 0.461 0.105 42.006 -2.260 0.381 3.160 0.147 -0.643 42.008 16 DD_G6C7:G4LV25_CC D 6 ? C 5 ? D 7 ? C 4 ? 1 D C 7 1_555 C G 4 1_555 D C 8 1_555 C G 3 1_555 -0.032 -1.967 3.334 0.088 4.159 29.741 -4.634 0.079 3.036 8.054 -0.171 30.024 17 DD_C7C8:G3G4_CC D 7 ? C 4 ? D 8 ? C 3 ? 1 D C 8 1_555 C G 3 1_555 D G 9 1_555 C C 2 1_555 -0.116 -1.961 3.376 -1.724 4.804 27.275 -5.228 -0.167 2.995 10.075 3.615 27.739 18 DD_C8G9:C2G3_CC D 8 ? C 3 ? D 9 ? C 2 ? 1 D G 9 1_555 C C 2 1_555 D G 10 1_555 C C 1 1_555 -0.005 -1.959 3.272 0.742 9.148 32.574 -4.731 0.119 2.640 15.919 -1.291 33.809 19 DD_G9G10:C1C2_CC D 9 ? C 2 ? D 10 ? C 1 ? # loop_ _pdbx_audit_support.country _pdbx_audit_support.funding_organization _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'United States' 'National Science Foundation (NSF, United States)' CHE-1845486 1 'United States' 'National Science Foundation (NSF, United States)' MCB-1715234 2 'United States' 'National Institutes of Health/National Cancer Institute (NIH/NCI)' 'Intramural Research Program' 3 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id LV2 _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id LV2 _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 4MS9 _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 none _pdbx_struct_assembly_auth_evidence.details ? #