data_6VEM # _entry.id 6VEM # _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 6VEM pdb_00006vem 10.2210/pdb6vem/pdb WWPDB D_1000246283 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6VEM _pdbx_database_status.recvd_initial_deposition_date 2020-01-02 _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 'Pallan, P.S.' 1 ? 'Egli, M.' 2 ? # _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 10101 _citation.page_last 10124 _citation.title ;Synthesis, chirality-dependent conformational and biological properties of siRNAs containing 5'-(R)- and 5'-(S)-C-methyl-guanosine. ; _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkaa750 _citation.pdbx_database_id_PubMed 32990754 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mikami, A.' 1 ? primary 'Erande, N.' 2 ? primary 'Matsuda, S.' 3 ? primary ;Kel'in, A. ; 4 ? primary 'Woods, L.B.' 5 ? primary 'Chickering, T.' 6 ? primary 'Pallan, P.S.' 7 ? primary 'Schlegel, M.K.' 8 ? primary 'Zlatev, I.' 9 ? primary 'Egli, M.' 10 ? primary 'Manoharan, M.' 11 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 6VEM _cell.details ? _cell.formula_units_Z ? _cell.length_a 37.921 _cell.length_a_esd ? _cell.length_b 37.921 _cell.length_b_esd ? _cell.length_c 57.852 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _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 6VEM _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' _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 'Modified Octamer RNA' 2570.619 2 ? ? ? 'GMX is 5 prime-C-methyl-guanosine' 2 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 5 ? ? ? ? 3 water nat water 18.015 30 ? ? ? ? # _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 'CCCC(GMX)GGG' _entity_poly.pdbx_seq_one_letter_code_can CCCCXGGG _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 C n 1 2 C n 1 3 C n 1 4 C n 1 5 GMX n 1 6 G n 1 7 G n 1 8 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 8 _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 6VEM _struct_ref.pdbx_db_accession 6VEM _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 6VEM A 1 ? 8 ? 6VEM 1 ? 8 ? 1 8 2 1 6VEM B 1 ? 8 ? 6VEM 9 ? 16 ? 9 16 # 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 GMX 'RNA linking' . '2-amino-9-(6-deoxy-5-O-phosphono-beta-D-allofuranosyl)-3,9-dihydro-6H-purin-6-one' ? 'C11 H16 N5 O8 P' 377.247 HOH non-polymer . WATER ? 'H2 O' 18.015 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 # _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 6VEM _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 2.34 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 47.34 _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 ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;Sodium cacodylate (20 mM, pH 6.0), sodium chloride (40 mM), hexamine cobalt(III) chloride (10 mM), and 2-methyl-2,4-pentanediol (MPD; 5% (v/v) ; _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 EIGER2 X 9M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-06-02 _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 0.9183 _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 21-ID-D' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9183 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-D _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6VEM _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.56 _reflns.d_resolution_low 23 _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 6721 _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 99.3 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 18.5 _reflns.pdbx_Rmerge_I_obs 0.063 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 63.3 _reflns.pdbx_netI_over_sigmaI 63.32 _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 ? _reflns.pdbx_Rpim_I_all .015 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.56 _reflns_shell.d_res_low 1.62 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.33 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 627 _reflns_shell.percent_possible_all 92.4 _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 0.869 _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 12.1 _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 ? _reflns_shell.pdbx_Rpim_I_all 0.243 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] 0.1400 _refine.aniso_B[1][2] 0.0700 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][2] 0.1400 _refine.aniso_B[2][3] -0.0000 _refine.aniso_B[3][3] -0.4400 _refine.B_iso_max 83.430 _refine.B_iso_mean 38.2930 _refine.B_iso_min 20.470 _refine.correlation_coeff_Fo_to_Fc 0.9760 _refine.correlation_coeff_Fo_to_Fc_free 0.9670 _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY' _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 6VEM _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 1.5600 _refine.ls_d_res_low 21.7200 _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 6392 _refine.ls_number_reflns_R_free 295 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.3300 _refine.ls_percent_reflns_R_free 4.4000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1799 _refine.ls_R_factor_R_free 0.2439 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1775 _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 0.000 _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 THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 259D _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.1080 _refine.pdbx_overall_ESU_R_Free 0.0980 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _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 ? _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 5.0460 _refine.overall_SU_ML 0.0770 _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 final _refine_hist.details ? _refine_hist.d_res_high 1.5600 _refine_hist.d_res_low 21.7200 _refine_hist.number_atoms_solvent 30 _refine_hist.number_atoms_total 405 _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 16 _refine_hist.pdbx_B_iso_mean_ligand 37.26 _refine_hist.pdbx_B_iso_mean_solvent 49.89 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 340 _refine_hist.pdbx_number_atoms_ligand 35 _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' ? 0.029 0.013 408 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 1.857 1.660 663 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 0.105 0.200 68 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.029 0.020 168 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 7.674 3.000 408 ? r_rigid_bond_restr ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.5620 _refine_ls_shell.d_res_low 1.6020 _refine_ls_shell.number_reflns_all 450 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 24 _refine_ls_shell.number_reflns_R_work 426 _refine_ls_shell.percent_reflns_obs 92.4000 _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 0.2680 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.2590 _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 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 6VEM _struct.title 'Structure of RNA octamer' _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 6VEM _struct_keywords.text ;Synthetic RNA, 5'-C-Metyl-guanosine, 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 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 3 ? I 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 covale1 covale both ? A C 4 "O3'" ? ? ? 1_555 A GMX 5 P ? ? A C 4 A GMX 5 1_555 ? ? ? ? ? ? ? 1.578 ? ? covale2 covale one ? A GMX 5 "O3'" ? ? ? 1_555 A G 6 P ? ? A GMX 5 A G 6 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale3 covale none ? D NCO . N3 ? ? ? 1_555 E NCO . N4 ? ? A NCO 102 A NCO 103 1_555 ? ? ? ? ? ? ? 1.545 ? ? covale4 covale none ? D NCO . N6 ? ? ? 1_555 E NCO . N4 ? ? A NCO 102 A NCO 103 1_555 ? ? ? ? ? ? ? 1.430 ? ? covale5 covale both ? B C 4 "O3'" ? ? ? 1_555 B GMX 5 P ? ? B C 12 B GMX 13 1_555 ? ? ? ? ? ? ? 1.586 ? ? covale6 covale one ? B GMX 5 "O3'" ? ? ? 1_555 B G 6 P ? ? B GMX 13 B G 14 1_555 ? ? ? ? ? ? ? 1.612 ? ? metalc1 metalc ? ? D NCO . CO ? ? ? 1_555 E NCO . N1 ? ? A NCO 102 A NCO 103 1_555 ? ? ? ? ? ? ? 2.562 ? ? metalc2 metalc ? ? D NCO . CO ? ? ? 1_555 E NCO . N4 ? ? A NCO 102 A NCO 103 1_555 ? ? ? ? ? ? ? 1.979 ? ? metalc3 metalc ? ? D NCO . N1 ? ? ? 1_555 E NCO . CO ? ? A NCO 102 A NCO 103 1_555 ? ? ? ? ? ? ? 2.292 ? ? metalc4 metalc ? ? D NCO . N3 ? ? ? 1_555 E NCO . CO ? ? A NCO 102 A NCO 103 1_555 ? ? ? ? ? ? ? 2.757 ? ? metalc5 metalc ? ? D NCO . N6 ? ? ? 1_555 E NCO . CO ? ? A NCO 102 A NCO 103 1_555 ? ? ? ? ? ? ? 2.479 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 1 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 1 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 1 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 3 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 3 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 3 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 6 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 6 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 6 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 7 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 7 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 7 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 8 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 8 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 8 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A NCO 101 ? 4 'binding site for residue NCO A 101' AC2 Software A NCO 104 ? 6 'binding site for residue NCO A 104' AC3 Software B NCO 101 ? 6 'binding site for residue NCO B 101' AC4 Software A NCO 102 ? 8 'binding site for residues NCO A 102 and NCO A 103' AC5 Software A NCO 102 ? 8 'binding site for residues NCO A 102 and NCO A 103' AC6 Software B C 12 ? 14 'binding site for Di-nucleotide C B 12 and GMX B 13' AC7 Software B GMX 13 ? 15 'binding site for Di-nucleotide GMX B 13 and G B 14' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 G A 8 ? G A 8 . ? 5_664 ? 2 AC1 4 G A 8 ? G A 8 . ? 1_555 ? 3 AC1 4 HOH H . ? HOH A 205 . ? 1_555 ? 4 AC1 4 G B 8 ? G B 16 . ? 5_654 ? 5 AC2 6 G A 6 ? G A 6 . ? 1_555 ? 6 AC2 6 G A 7 ? G A 7 . ? 1_555 ? 7 AC2 6 G B 6 ? G B 14 . ? 3_654 ? 8 AC2 6 G B 7 ? G B 15 . ? 3_654 ? 9 AC2 6 G B 8 ? G B 16 . ? 3_654 ? 10 AC2 6 HOH I . ? HOH B 202 . ? 3_654 ? 11 AC3 6 NCO D . ? NCO A 102 . ? 2_545 ? 12 AC3 6 NCO E . ? NCO A 103 . ? 2_545 ? 13 AC3 6 C B 4 ? C B 12 . ? 1_555 ? 14 AC3 6 GMX B 5 ? GMX B 13 . ? 1_555 ? 15 AC3 6 HOH I . ? HOH B 201 . ? 1_555 ? 16 AC3 6 HOH I . ? HOH B 203 . ? 1_555 ? 17 AC4 8 GMX A 5 ? GMX A 5 . ? 1_555 ? 18 AC4 8 G A 6 ? G A 6 . ? 1_555 ? 19 AC4 8 G A 7 ? G A 7 . ? 1_555 ? 20 AC4 8 G A 8 ? G A 8 . ? 1_555 ? 21 AC4 8 HOH H . ? HOH A 208 . ? 1_555 ? 22 AC4 8 C B 1 ? C B 9 . ? 1_555 ? 23 AC4 8 G B 8 ? G B 16 . ? 5_654 ? 24 AC4 8 NCO G . ? NCO B 101 . ? 3_654 ? 25 AC5 8 GMX A 5 ? GMX A 5 . ? 1_555 ? 26 AC5 8 G A 6 ? G A 6 . ? 1_555 ? 27 AC5 8 G A 7 ? G A 7 . ? 1_555 ? 28 AC5 8 G A 8 ? G A 8 . ? 1_555 ? 29 AC5 8 HOH H . ? HOH A 208 . ? 1_555 ? 30 AC5 8 C B 1 ? C B 9 . ? 1_555 ? 31 AC5 8 G B 8 ? G B 16 . ? 5_654 ? 32 AC5 8 NCO G . ? NCO B 101 . ? 3_654 ? 33 AC6 14 C A 2 ? C A 2 . ? 6_555 ? 34 AC6 14 C A 3 ? C A 3 . ? 6_555 ? 35 AC6 14 C A 4 ? C A 4 . ? 1_555 ? 36 AC6 14 GMX A 5 ? GMX A 5 . ? 1_555 ? 37 AC6 14 G A 6 ? G A 6 . ? 1_555 ? 38 AC6 14 C B 3 ? C B 11 . ? 1_555 ? 39 AC6 14 G B 6 ? G B 14 . ? 1_555 ? 40 AC6 14 NCO G . ? NCO B 101 . ? 1_555 ? 41 AC6 14 HOH I . ? HOH B 201 . ? 1_555 ? 42 AC6 14 HOH I . ? HOH B 203 . ? 1_555 ? 43 AC6 14 HOH I . ? HOH B 205 . ? 1_555 ? 44 AC6 14 HOH I . ? HOH B 209 . ? 1_555 ? 45 AC6 14 HOH I . ? HOH B 211 . ? 1_555 ? 46 AC6 14 HOH I . ? HOH B 212 . ? 1_555 ? 47 AC7 15 C A 2 ? C A 2 . ? 6_555 ? 48 AC7 15 C A 3 ? C A 3 . ? 6_555 ? 49 AC7 15 C A 3 ? C A 3 . ? 1_555 ? 50 AC7 15 C A 4 ? C A 4 . ? 1_555 ? 51 AC7 15 GMX A 5 ? GMX A 5 . ? 1_555 ? 52 AC7 15 NCO F . ? NCO A 104 . ? 2_545 ? 53 AC7 15 C B 4 ? C B 12 . ? 1_555 ? 54 AC7 15 G B 7 ? G B 15 . ? 1_555 ? 55 AC7 15 NCO G . ? NCO B 101 . ? 1_555 ? 56 AC7 15 HOH I . ? HOH B 201 . ? 1_555 ? 57 AC7 15 HOH I . ? HOH B 203 . ? 1_555 ? 58 AC7 15 HOH I . ? HOH B 204 . ? 1_555 ? 59 AC7 15 HOH I . ? HOH B 207 . ? 1_555 ? 60 AC7 15 HOH I . ? HOH B 209 . ? 1_555 ? 61 AC7 15 HOH I . ? HOH B 212 . ? 1_555 ? # _atom_sites.entry_id 6VEM _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] 0.026371 _atom_sites.fract_transf_matrix[1][2] 0.015225 _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] 0.030450 _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] 0.017285 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C CO N O P # loop_ _database_PDB_caveat.text 'NCO A103 has occupancy of 0.1' # 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 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 GMX 5 5 5 GMX GMX A . n A 1 6 G 6 6 6 G G A . n A 1 7 G 7 7 7 G G A . n A 1 8 G 8 8 8 G G A . n B 1 1 C 1 9 9 C C B . n B 1 2 C 2 10 10 C C B . n B 1 3 C 3 11 11 C C B . n B 1 4 C 4 12 12 C C B . n B 1 5 GMX 5 13 13 GMX GMX B . n B 1 6 G 6 14 14 G G B . n B 1 7 G 7 15 15 G G B . n B 1 8 G 8 16 16 G G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 NCO 1 101 1 NCO NCO A . D 2 NCO 1 102 2 NCO NCO A . E 2 NCO 1 103 3 NCO NCO A . F 2 NCO 1 104 4 NCO NCO A . G 2 NCO 1 101 5 NCO NCO B . H 3 HOH 1 201 29 HOH HOH A . H 3 HOH 2 202 19 HOH HOH A . H 3 HOH 3 203 32 HOH HOH A . H 3 HOH 4 204 26 HOH HOH A . H 3 HOH 5 205 35 HOH HOH A . H 3 HOH 6 206 28 HOH HOH A . H 3 HOH 7 207 30 HOH HOH A . H 3 HOH 8 208 9 HOH HOH A . H 3 HOH 9 209 11 HOH HOH A . H 3 HOH 10 210 18 HOH HOH A . H 3 HOH 11 211 15 HOH HOH A . H 3 HOH 12 212 7 HOH HOH A . H 3 HOH 13 213 34 HOH HOH A . I 3 HOH 1 201 6 HOH HOH B . I 3 HOH 2 202 23 HOH HOH B . I 3 HOH 3 203 24 HOH HOH B . I 3 HOH 4 204 20 HOH HOH B . I 3 HOH 5 205 12 HOH HOH B . I 3 HOH 6 206 17 HOH HOH B . I 3 HOH 7 207 27 HOH HOH B . I 3 HOH 8 208 33 HOH HOH B . I 3 HOH 9 209 21 HOH HOH B . I 3 HOH 10 210 13 HOH HOH B . I 3 HOH 11 211 14 HOH HOH B . I 3 HOH 12 212 25 HOH HOH B . I 3 HOH 13 213 16 HOH HOH B . I 3 HOH 14 214 8 HOH HOH B . I 3 HOH 15 215 22 HOH HOH B . I 3 HOH 16 216 10 HOH HOH B . I 3 HOH 17 217 31 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # 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)' 1880 ? 1 MORE -7 ? 1 'SSA (A^2)' 3200 ? # _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_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N1 ? D NCO . ? A NCO 102 ? 1_555 25.5 ? 2 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N2 ? D NCO . ? A NCO 102 ? 1_555 156.7 ? 3 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N2 ? D NCO . ? A NCO 102 ? 1_555 177.6 ? 4 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 66.8 ? 5 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 91.5 ? 6 N2 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 90.9 ? 7 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? D NCO . ? A NCO 102 ? 1_555 85.0 ? 8 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? D NCO . ? A NCO 102 ? 1_555 90.7 ? 9 N2 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? D NCO . ? A NCO 102 ? 1_555 88.7 ? 10 N3 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? D NCO . ? A NCO 102 ? 1_555 90.9 ? 11 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N5 ? D NCO . ? A NCO 102 ? 1_555 111.9 ? 12 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N5 ? D NCO . ? A NCO 102 ? 1_555 86.8 ? 13 N2 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N5 ? D NCO . ? A NCO 102 ? 1_555 90.9 ? 14 N3 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N5 ? D NCO . ? A NCO 102 ? 1_555 174.8 ? 15 N4 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N5 ? D NCO . ? A NCO 102 ? 1_555 94.0 ? 16 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 92.1 ? 17 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 86.7 ? 18 N2 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 93.9 ? 19 N3 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 87.9 ? 20 N4 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 177.1 ? 21 N5 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 87.2 ? 22 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 80.5 ? 23 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 93.1 ? 24 N2 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 88.9 ? 25 N3 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 46.0 ? 26 N4 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 136.7 ? 27 N5 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 129.2 ? 28 N6 ? D NCO . ? A NCO 102 ? 1_555 CO ? D NCO . ? A NCO 102 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 42.3 ? 29 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N1 ? E NCO . ? A NCO 103 ? 1_555 29.9 ? 30 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N2 ? E NCO . ? A NCO 103 ? 1_555 153.3 ? 31 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N2 ? E NCO . ? A NCO 103 ? 1_555 176.8 ? 32 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? E NCO . ? A NCO 103 ? 1_555 123.0 ? 33 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? E NCO . ? A NCO 103 ? 1_555 95.7 ? 34 N2 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? E NCO . ? A NCO 103 ? 1_555 81.2 ? 35 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 79.7 ? 36 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 88.6 ? 37 N2 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 92.1 ? 38 N3 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N4 ? E NCO . ? A NCO 103 ? 1_555 86.2 ? 39 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N5 ? E NCO . ? A NCO 103 ? 1_555 59.7 ? 40 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N5 ? E NCO . ? A NCO 103 ? 1_555 87.3 ? 41 N2 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N5 ? E NCO . ? A NCO 103 ? 1_555 95.8 ? 42 N3 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N5 ? E NCO . ? A NCO 103 ? 1_555 176.9 ? 43 N4 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N5 ? E NCO . ? A NCO 103 ? 1_555 93.2 ? 44 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? E NCO . ? A NCO 103 ? 1_555 100.5 ? 45 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? E NCO . ? A NCO 103 ? 1_555 91.4 ? 46 N2 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? E NCO . ? A NCO 103 ? 1_555 87.8 ? 47 N3 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? E NCO . ? A NCO 103 ? 1_555 93.4 ? 48 N4 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? E NCO . ? A NCO 103 ? 1_555 179.6 ? 49 N5 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? E NCO . ? A NCO 103 ? 1_555 87.2 ? 50 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 68.1 ? 51 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 62.2 ? 52 N2 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 117.3 ? 53 N3 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 69.9 ? 54 N4 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 34.1 ? 55 N5 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 111.2 ? 56 N6 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 102 ? 1_555 145.7 ? 57 N1 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 69.9 ? 58 N1 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 93.6 ? 59 N2 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 88.8 ? 60 N3 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 120.0 ? 61 N4 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 34.9 ? 62 N5 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 59.0 ? 63 N6 ? E NCO . ? A NCO 103 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 145.5 ? 64 N3 ? D NCO . ? A NCO 102 ? 1_555 CO ? E NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 102 ? 1_555 63.2 ? # 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 2020-11-18 2 'Structure model' 1 1 2023-10-11 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 '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' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 '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' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' # 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 ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0257 1 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.25 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? MOLREP ? ? ? CCP4 5 # _pdbx_entry_details.entry_id 6VEM _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 GMX OP2 O N N 74 GMX P P N N 75 GMX OP1 O N N 76 GMX "O5'" O N N 77 GMX "C5'" C N R 78 GMX "C6'" C N N 79 GMX "C4'" C N S 80 GMX "O4'" O N N 81 GMX "C1'" C N R 82 GMX "C2'" C N R 83 GMX "O2'" O N N 84 GMX "C3'" C N S 85 GMX "O3'" O N N 86 GMX N9 N Y N 87 GMX C8 C Y N 88 GMX N7 N Y N 89 GMX C5 C Y N 90 GMX C6 C N N 91 GMX O6 O N N 92 GMX N1 N N N 93 GMX C2 C N N 94 GMX N2 N N N 95 GMX N3 N N N 96 GMX C4 C Y N 97 GMX H1 H N N 98 GMX H2 H N N 99 GMX H3 H N N 100 GMX H4 H N N 101 GMX H5 H N N 102 GMX H6 H N N 103 GMX H7 H N N 104 GMX H8 H N N 105 GMX H9 H N N 106 GMX H10 H N N 107 GMX H11 H N N 108 GMX H12 H N N 109 GMX H13 H N N 110 GMX H14 H N N 111 GMX H15 H N N 112 GMX H16 H N N 113 GMX OP3 O N N 114 HOH O O N N 115 HOH H1 H N N 116 HOH H2 H N N 117 NCO CO CO N N 118 NCO N1 N N N 119 NCO N2 N N N 120 NCO N3 N N N 121 NCO N4 N N N 122 NCO N5 N N N 123 NCO N6 N N N 124 NCO HN11 H N N 125 NCO HN12 H N N 126 NCO HN13 H N N 127 NCO HN21 H N N 128 NCO HN22 H N N 129 NCO HN23 H N N 130 NCO HN31 H N N 131 NCO HN32 H N N 132 NCO HN33 H N N 133 NCO HN41 H N N 134 NCO HN42 H N N 135 NCO HN43 H N N 136 NCO HN51 H N N 137 NCO HN52 H N N 138 NCO HN53 H N N 139 NCO HN61 H N N 140 NCO HN62 H N N 141 NCO HN63 H N N 142 # 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 GMX "C6'" "C5'" sing N N 77 GMX OP1 P sing N N 78 GMX "O3'" "C3'" sing N N 79 GMX "C5'" "O5'" sing N N 80 GMX "C5'" "C4'" sing N N 81 GMX P "O5'" sing N N 82 GMX P OP2 sing N N 83 GMX "C4'" "C3'" sing N N 84 GMX "C4'" "O4'" sing N N 85 GMX "C3'" "C2'" sing N N 86 GMX "O2'" "C2'" sing N N 87 GMX "O4'" "C1'" sing N N 88 GMX "C2'" "C1'" sing N N 89 GMX "C1'" N9 sing N N 90 GMX C8 N9 sing Y N 91 GMX C8 N7 doub Y N 92 GMX N9 C4 sing Y N 93 GMX N7 C5 sing Y N 94 GMX C4 N3 sing N N 95 GMX C4 C5 doub Y N 96 GMX N3 C2 sing N N 97 GMX C5 C6 sing N N 98 GMX C2 N2 sing N N 99 GMX C2 N1 doub N N 100 GMX C6 N1 sing N N 101 GMX C6 O6 doub N N 102 GMX OP2 H1 sing N N 103 GMX OP1 H2 sing N N 104 GMX "C5'" H3 sing N N 105 GMX "C6'" H4 sing N N 106 GMX "C6'" H5 sing N N 107 GMX "C6'" H6 sing N N 108 GMX "C4'" H7 sing N N 109 GMX "C1'" H8 sing N N 110 GMX "C2'" H9 sing N N 111 GMX "O2'" H10 sing N N 112 GMX "C3'" H11 sing N N 113 GMX "O3'" H12 sing N N 114 GMX C8 H13 sing N N 115 GMX N2 H14 sing N N 116 GMX N2 H15 sing N N 117 GMX N3 H16 sing N N 118 GMX P OP3 doub N N 119 HOH O H1 sing N N 120 HOH O H2 sing N N 121 NCO CO N1 sing N N 122 NCO CO N2 sing N N 123 NCO CO N3 sing N N 124 NCO CO N4 sing N N 125 NCO CO N5 sing N N 126 NCO CO N6 sing N N 127 NCO N1 HN11 sing N N 128 NCO N1 HN12 sing N N 129 NCO N1 HN13 sing N N 130 NCO N2 HN21 sing N N 131 NCO N2 HN22 sing N N 132 NCO N2 HN23 sing N N 133 NCO N3 HN31 sing N N 134 NCO N3 HN32 sing N N 135 NCO N3 HN33 sing N N 136 NCO N4 HN41 sing N N 137 NCO N4 HN42 sing N N 138 NCO N4 HN43 sing N N 139 NCO N5 HN51 sing N N 140 NCO N5 HN52 sing N N 141 NCO N5 HN53 sing N N 142 NCO N6 HN61 sing N N 143 NCO N6 HN62 sing N N 144 NCO N6 HN63 sing N N 145 # _ndb_struct_conf_na.entry_id 6VEM _ndb_struct_conf_na.feature '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 A C 1 1_555 B G 8 1_555 0.028 -0.165 0.145 5.643 -12.676 -0.668 1 A_C1:G16_B A 1 ? B 16 ? 19 1 1 A C 2 1_555 B G 7 1_555 0.197 -0.190 -0.063 13.347 -10.679 1.207 2 A_C2:G15_B A 2 ? B 15 ? 19 1 1 A C 3 1_555 B G 6 1_555 0.285 -0.197 -0.248 10.898 -8.608 1.794 3 A_C3:G14_B A 3 ? B 14 ? 19 1 1 A G 6 1_555 B C 3 1_555 -0.450 -0.158 0.012 -1.851 -11.258 1.251 4 A_G6:C11_B A 6 ? B 11 ? 19 1 1 A G 7 1_555 B C 2 1_555 -0.184 -0.248 -0.219 -13.947 -16.530 -1.038 5 A_G7:C10_B A 7 ? B 10 ? 19 1 1 A G 8 1_555 B C 1 1_555 -0.181 -0.327 0.020 -13.832 -10.352 -1.477 6 A_G8:C9_B A 8 ? B 9 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 B G 8 1_555 A C 2 1_555 B G 7 1_555 -0.568 -1.618 3.223 -3.509 1.512 30.425 -3.353 0.395 3.185 2.867 6.654 30.658 1 AA_C1C2:G15G16_BB A 1 ? B 16 ? A 2 ? B 15 ? 1 A C 2 1_555 B G 7 1_555 A C 3 1_555 B G 6 1_555 0.008 -1.961 3.363 -1.514 5.510 30.455 -4.709 -0.300 2.967 10.374 2.850 30.974 2 AA_C2C3:G14G15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A G 6 1_555 B C 3 1_555 A G 7 1_555 B C 2 1_555 0.469 -1.935 3.494 3.880 11.344 36.137 -4.402 -0.231 2.816 17.698 -6.053 38.011 3 AA_G6G7:C10C11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A G 7 1_555 B C 2 1_555 A G 8 1_555 B C 1 1_555 0.610 -1.744 3.239 2.727 8.992 31.281 -4.552 -0.648 2.690 16.223 -4.919 32.628 4 AA_G7G8:C9C10_BB A 7 ? B 10 ? A 8 ? B 9 ? # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id GMX _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id GMX _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 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT HEXAMMINE(III)' NCO 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 259D _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 ? #