data_9CKH # _entry.id 9CKH # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.404 _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 9CKH pdb_00009ckh 10.2210/pdb9ckh/pdb WWPDB D_1000285739 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2025-07-30 _pdbx_audit_revision_history.part_number ? # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9CKH _pdbx_database_status.recvd_initial_deposition_date 2024-07-08 _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 # _pdbx_database_related.db_name PDB _pdbx_database_related.details 'Similar motif without Ag+' _pdbx_database_related.db_id 9C6U _pdbx_database_related.content_type unspecified # _pdbx_contact_author.id 2 _pdbx_contact_author.email rs17@nyu.edu _pdbx_contact_author.name_first Ruojie _pdbx_contact_author.name_last Sha _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-0807-734X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Vecchioni, S.' 1 0000-0001-8243-650X 'Jong, M.A.' 2 ? 'Woloszyn, K.' 3 0000-0003-1200-583X 'Sha, R.' 4 0000-0002-0807-734X 'Ohayon, Y.P.' 5 0000-0001-7500-4282 'Gallindo, M.A.' 6 0000-0003-4355-4313 'Lopez Chamorro, C.' 7 0009-0000-0416-6866 # _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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Deazapurine metal-mediated nanostructures' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lopez Chamorro, C.' 1 ? primary 'Jong, M.A.' 2 ? # 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 ;DNA (5'-D(*GP*AP*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3') ; 6447.306 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3') ; 2079.436 1 ? ? ? ? 3 polymer syn ;DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3') ; 1825.216 1 ? ? ? ? 4 polymer syn ;DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3') ; 2432.614 1 ? ? ? ? 5 non-polymer syn 'SILVER ION' 107.868 2 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes ;(DG)(DA)(7GU)(DC)(7DA)(7GU)(DC)(DC)(DT)(7GU)(DT)(7DA)(DC)(7GU)(7GU)(7DA)(DC) (7DA)(DT)(DC)(7DA) ; GAGCAGCCTGTACGGACATCA A ? 2 polydeoxyribonucleotide no yes '(DC)(DC)(7GU)(DT)(7DA)(DC)(7DA)' CCGTACA B ? 3 polydeoxyribonucleotide no no '(DG)(DG)(DC)(DT)(DG)(DC)' GGCTGC C ? 4 polydeoxyribonucleotide no no '(DT)(DC)(DT)(DG)(DA)(DT)(DG)(DT)' TCTGATGT D ? # _pdbx_entity_nonpoly.entity_id 5 _pdbx_entity_nonpoly.name 'SILVER ION' _pdbx_entity_nonpoly.comp_id AG # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DA n 1 3 7GU n 1 4 DC n 1 5 7DA n 1 6 7GU n 1 7 DC n 1 8 DC n 1 9 DT n 1 10 7GU n 1 11 DT n 1 12 7DA n 1 13 DC n 1 14 7GU n 1 15 7GU n 1 16 7DA n 1 17 DC n 1 18 7DA n 1 19 DT n 1 20 DC n 1 21 7DA n 2 1 DC n 2 2 DC n 2 3 7GU n 2 4 DT n 2 5 7DA n 2 6 DC n 2 7 7DA n 3 1 DG n 3 2 DG n 3 3 DC n 3 4 DT n 3 5 DG n 3 6 DC n 4 1 DT n 4 2 DC n 4 3 DT n 4 4 DG n 4 5 DA n 4 6 DT n 4 7 DG n 4 8 DT n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 21 'synthetic construct' ? 32630 ? 2 1 sample 1 7 'synthetic construct' ? 32630 ? 3 1 sample 1 6 'synthetic construct' ? 32630 ? 4 1 sample 1 8 'synthetic construct' ? 32630 ? # 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 7DA 'DNA linking' n "7-DEAZA-2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C11 H15 N4 O6 P' 330.234 7GU 'DNA linking' n "7-DEAZA-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C11 H15 N4 O7 P' 346.233 AG non-polymer . 'SILVER ION' ? 'Ag 1' 107.868 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # 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 DG 1 101 101 DG DG A . n A 1 2 DA 2 102 102 DA DA A . n A 1 3 7GU 3 103 103 7GU 7GU A . n A 1 4 DC 4 104 104 DC DC A . n A 1 5 7DA 5 105 105 7DA 7DA A . n A 1 6 7GU 6 106 106 7GU 7GU A . n A 1 7 DC 7 107 107 DC DC A . n A 1 8 DC 8 108 108 DC DC A . n A 1 9 DT 9 109 109 DT DT A . n A 1 10 7GU 10 110 110 7GU 7GU A . n A 1 11 DT 11 111 111 DT DT A . n A 1 12 7DA 12 112 112 7DA 7DA A . n A 1 13 DC 13 113 113 DC DC A . n A 1 14 7GU 14 114 114 7GU 7GU A . n A 1 15 7GU 15 115 115 7GU 7GU A . n A 1 16 7DA 16 116 116 7DA 7DA A . n A 1 17 DC 17 117 117 DC DC A . n A 1 18 7DA 18 118 118 7DA 7DA A . n A 1 19 DT 19 119 119 DT DT A . n A 1 20 DC 20 120 120 DC DC A . n A 1 21 7DA 21 121 121 7DA 7DA A . n B 2 1 DC 1 119 119 DC DC B . n B 2 2 DC 2 120 120 DC DC B . n B 2 3 7GU 3 121 121 7GU 7GU B . n B 2 4 DT 4 122 122 DT DT B . n B 2 5 7DA 5 123 123 7DA 7DA B . n B 2 6 DC 6 124 124 DC DC B . n B 2 7 7DA 7 125 125 7DA 7DA B . n C 3 1 DG 1 209 209 DG DG C . n C 3 2 DG 2 210 210 DG DG C . n C 3 3 DC 3 211 211 DC DC C . n C 3 4 DT 4 212 212 DT DT C . n C 3 5 DG 5 213 213 DG DG C . n C 3 6 DC 6 214 214 DC DC C . n D 4 1 DT 1 201 201 DT DT D . n D 4 2 DC 2 202 202 DC DC D . n D 4 3 DT 3 203 203 DT DT D . n D 4 4 DG 4 204 204 DG DG D . n D 4 5 DA 5 205 205 DA DA D . n D 4 6 DT 6 206 206 DT DT D . n D 4 7 DG 7 207 207 DG DG D . n D 4 8 DT 8 208 208 DT DT D . n # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 7DA ? ? 7DA ? ? 'SUBJECT OF INVESTIGATION' ? 2 7GU ? ? 7GU ? ? 'SUBJECT OF INVESTIGATION' ? 3 AG ? ? AG ? ? 'SUBJECT OF INVESTIGATION' ? # 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 5 AG 1 201 2 AG AG A . F 5 AG 1 301 1 AG AG D . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? STARANISO ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 4 # _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 9CKH _cell.details ? _cell.formula_units_Z ? _cell.length_a 123.277 _cell.length_a_esd ? _cell.length_b 123.277 _cell.length_b_esd ? _cell.length_c 62.265 _cell.length_c_esd ? _cell.volume 819480.716 _cell.volume_esd ? _cell.Z_PDB 6 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9CKH _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall 'P 6c' _symmetry.space_group_name_H-M 'P 63' _symmetry.pdbx_full_space_group_name_H-M ? # _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 9CKH _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 ? _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol ? _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.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details '338-293 at 0.4 degree /hr' _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '100 mM MOPS, 1.25 M magnesium sulfate' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _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 2024-06-23 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.979346 _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 'NSLS-II BEAMLINE 17-ID-2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.979346 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 17-ID-2 _diffrn_source.pdbx_synchrotron_site NSLS-II # _reflns.B_iso_Wilson_estimate 244.23 _reflns.entry_id 9CKH _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 5.92 _reflns.d_resolution_low 19.670 _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 2128 _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 86.7 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.6 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 8.9 _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 ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _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 _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 _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 5.922 6.737 ? 1.1 ? ? ? ? 192 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0.563 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 11.101 19.670 ? 27.6 ? ? ? ? 192 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 0.999 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 260.18 _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 9CKH _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 5.92 _refine.ls_d_res_low 19.67 _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 2128 _refine.ls_number_reflns_R_free 114 _refine.ls_number_reflns_R_work 2014 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 78.99 _refine.ls_percent_reflns_R_free 5.36 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1621 _refine.ls_R_factor_R_free 0.1793 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1605 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.98 _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 SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 20.8478 _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 0.8329 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 5.92 _refine_hist.d_res_low 19.67 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 857 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 855 _refine_hist.pdbx_number_atoms_ligand 2 _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' ? 0.0084 ? 956 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.4527 ? 1467 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0656 ? 153 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0058 ? 42 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 38.7412 ? 354 ? f_dihedral_angle_d ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 5.92 _refine_ls_shell.d_res_low 19.67 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 114 _refine_ls_shell.number_reflns_R_work 2014 _refine_ls_shell.percent_reflns_obs 78.99 _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_error ? _refine_ls_shell.R_factor_R_work 0.1605 _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 ? _refine_ls_shell.R_factor_R_free 0.1793 # _struct.entry_id 9CKH _struct.title '[d2d3-2Ag] Tensegrity triangle with deazapurines on the helical and center strands with two deazaA:Ag+:T base pairs' _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 9CKH _struct_keywords.text 'Tensegrity triangle, deaza, Ag+, mmDNA, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 5 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 9CKH 9CKH ? 1 ? 1 2 PDB 9CKH 9CKH ? 2 ? 1 3 PDB 9CKH 9CKH ? 3 ? 1 4 PDB 9CKH 9CKH ? 4 ? 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 9CKH A 1 ? 21 ? 9CKH 101 ? 121 ? 101 121 2 2 9CKH B 1 ? 7 ? 9CKH 119 ? 125 ? 119 125 3 3 9CKH C 1 ? 6 ? 9CKH 209 ? 214 ? 209 214 4 4 9CKH D 1 ? 8 ? 9CKH 201 ? 208 ? 201 208 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D,E,F 1 2 A,B,C,D,E,F 1 3 A,B,C,D,E,F # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5000000000 -0.8660254038 0.0000000000 -61.6385000000 0.8660254038 -0.5000000000 0.0000000000 106.7610137023 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5000000000 0.8660254038 0.0000000000 -123.2770000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # 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 DA 2 "O3'" ? ? ? 1_555 A 7GU 3 P ? ? A DA 102 A 7GU 103 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale2 covale both ? A 7GU 3 "O3'" ? ? ? 1_555 A DC 4 P ? ? A 7GU 103 A DC 104 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale3 covale both ? A DC 4 "O3'" ? ? ? 1_555 A 7DA 5 P ? ? A DC 104 A 7DA 105 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale4 covale both ? A 7DA 5 "O3'" ? ? ? 1_555 A 7GU 6 P ? ? A 7DA 105 A 7GU 106 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale5 covale both ? A 7GU 6 "O3'" ? ? ? 1_555 A DC 7 P ? ? A 7GU 106 A DC 107 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale6 covale both ? A DT 9 "O3'" ? ? ? 1_555 A 7GU 10 P ? ? A DT 109 A 7GU 110 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale7 covale both ? A 7GU 10 "O3'" ? ? ? 1_555 A DT 11 P ? ? A 7GU 110 A DT 111 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale8 covale both ? A DT 11 "O3'" ? ? ? 1_555 A 7DA 12 P ? ? A DT 111 A 7DA 112 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale9 covale both ? A 7DA 12 "O3'" ? ? ? 1_555 A DC 13 P ? ? A 7DA 112 A DC 113 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale10 covale both ? A DC 13 "O3'" ? ? ? 1_555 A 7GU 14 P ? ? A DC 113 A 7GU 114 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale11 covale both ? A 7GU 14 "O3'" ? ? ? 1_555 A 7GU 15 P ? ? A 7GU 114 A 7GU 115 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale12 covale both ? A 7GU 15 "O3'" ? ? ? 1_555 A 7DA 16 P ? ? A 7GU 115 A 7DA 116 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale13 covale both ? A 7DA 16 "O3'" ? ? ? 1_555 A DC 17 P ? ? A 7DA 116 A DC 117 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale14 covale both ? A DC 17 "O3'" ? ? ? 1_555 A 7DA 18 P ? ? A DC 117 A 7DA 118 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale15 covale both ? A 7DA 18 "O3'" ? ? ? 1_555 A DT 19 P ? ? A 7DA 118 A DT 119 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale16 covale both ? A DC 20 "O3'" ? ? ? 1_555 A 7DA 21 P ? ? A DC 120 A 7DA 121 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale17 covale both ? B DC 2 "O3'" ? ? ? 1_555 B 7GU 3 P ? ? B DC 120 B 7GU 121 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale18 covale both ? B 7GU 3 "O3'" ? ? ? 1_555 B DT 4 P ? ? B 7GU 121 B DT 122 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale19 covale both ? B DT 4 "O3'" ? ? ? 1_555 B 7DA 5 P ? ? B DT 122 B 7DA 123 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale20 covale both ? B 7DA 5 "O3'" ? ? ? 1_555 B DC 6 P ? ? B 7DA 123 B DC 124 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale21 covale both ? B DC 6 "O3'" ? ? ? 1_555 B 7DA 7 P ? ? B DC 124 B 7DA 125 1_555 ? ? ? ? ? ? ? 1.610 ? ? metalc1 metalc ? ? A DT 11 N3 ? ? ? 1_555 E AG . AG ? ? A DT 111 A AG 201 1_555 ? ? ? ? ? ? ? 2.100 ? ? metalc2 metalc ? ? A 7DA 16 N1 ? ? ? 1_555 F AG . AG ? ? A 7DA 116 D AG 301 1_555 ? ? ? ? ? ? ? 2.114 ? ? metalc3 metalc ? ? E AG . AG ? ? ? 1_555 B 7DA 5 N1 ? ? A AG 201 B 7DA 123 1_555 ? ? ? ? ? ? ? 2.100 ? ? metalc4 metalc ? ? D DT 8 N3 ? ? ? 1_555 F AG . AG ? ? D DT 208 D AG 301 1_555 ? ? ? ? ? ? ? 2.120 ? ? hydrog1 hydrog ? ? A DA 2 N1 ? ? ? 1_555 C DC 6 N4 ? ? A DA 102 C DC 214 1_555 ? ? ? ? ? ? 'DA-DC MISPAIR' ? ? ? hydrog2 hydrog ? ? A 7GU 3 N1 ? ? ? 1_555 C DC 6 N3 ? ? A 7GU 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A 7GU 3 N2 ? ? ? 1_555 C DC 6 O2 ? ? A 7GU 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A 7GU 3 O6 ? ? ? 1_555 C DC 6 N4 ? ? A 7GU 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 4 N3 ? ? ? 1_555 C DG 5 N1 ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DG 5 O6 ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 4 O2 ? ? ? 1_555 C DG 5 N2 ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A 7DA 5 N1 ? ? ? 1_555 C DT 4 N3 ? ? A 7DA 105 C DT 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A 7DA 5 N6 ? ? ? 1_555 C DT 4 O4 ? ? A 7DA 105 C DT 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 7GU 6 N1 ? ? ? 1_555 C DC 3 N3 ? ? A 7GU 106 C DC 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A 7GU 6 N2 ? ? ? 1_555 C DC 3 O2 ? ? A 7GU 106 C DC 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A 7GU 6 O6 ? ? ? 1_555 C DC 3 N4 ? ? A 7GU 106 C DC 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 7 N3 ? ? ? 1_555 C DG 2 N2 ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog14 hydrog ? ? A DC 7 O2 ? ? ? 1_555 C DG 2 N1 ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog15 hydrog ? ? A DC 8 N3 ? ? ? 1_555 C DG 1 N1 ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 N4 ? ? ? 1_555 C DG 1 O6 ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 8 O2 ? ? ? 1_555 C DG 1 N2 ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B 7DA 7 N1 ? ? A DT 109 B 7DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B 7DA 7 N6 ? ? A DT 109 B 7DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A 7GU 10 N1 ? ? ? 1_555 B DC 6 N3 ? ? A 7GU 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A 7GU 10 N2 ? ? ? 1_555 B DC 6 O2 ? ? A 7GU 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 7GU 10 O6 ? ? ? 1_555 B DC 6 N4 ? ? A 7GU 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A 7DA 12 N1 ? ? ? 1_555 B DT 4 N3 ? ? A 7DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A 7DA 12 N6 ? ? ? 1_555 B DT 4 O4 ? ? A 7DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B 7GU 3 N1 ? ? A DC 113 B 7GU 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B 7GU 3 O6 ? ? A DC 113 B 7GU 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B 7GU 3 N2 ? ? A DC 113 B 7GU 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A 7GU 14 N1 ? ? ? 1_555 B DC 2 N3 ? ? A 7GU 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A 7GU 14 N2 ? ? ? 1_555 B DC 2 O2 ? ? A 7GU 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A 7GU 14 O6 ? ? ? 1_555 B DC 2 N4 ? ? A 7GU 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A 7GU 15 N1 ? ? ? 1_555 B DC 1 N3 ? ? A 7GU 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A 7GU 15 N2 ? ? ? 1_555 B DC 1 O2 ? ? A 7GU 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A 7GU 15 O6 ? ? ? 1_555 B DC 1 N4 ? ? A 7GU 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DC 17 N3 ? ? ? 1_555 D DG 7 N1 ? ? A DC 117 D DG 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DC 17 N4 ? ? ? 1_555 D DG 7 O6 ? ? A DC 117 D DG 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DC 17 O2 ? ? ? 1_555 D DG 7 N2 ? ? A DC 117 D DG 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A 7DA 18 N1 ? ? ? 1_555 D DT 6 N3 ? ? A 7DA 118 D DT 206 1_555 ? ? ? ? ? ? '7DA-DT MISPAIR' ? ? ? hydrog38 hydrog ? ? A DT 19 N3 ? ? ? 1_555 D DA 5 N1 ? ? A DT 119 D DA 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A DT 19 O4 ? ? ? 1_555 D DA 5 N6 ? ? A DT 119 D DA 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A DC 20 N3 ? ? ? 1_555 D DG 4 N2 ? ? A DC 120 D DG 204 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog41 hydrog ? ? A DC 20 O2 ? ? ? 1_555 D DG 4 N1 ? ? A DC 120 D DG 204 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog42 hydrog ? ? A 7DA 21 N1 ? ? ? 1_555 D DT 3 N3 ? ? A 7DA 121 D DT 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A 7DA 21 N6 ? ? ? 1_555 D DT 3 O4 ? ? A 7DA 121 D DT 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # 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 N3 ? A DT 11 ? A DT 111 ? 1_555 AG ? E AG . ? A AG 201 ? 1_555 N1 ? B 7DA 5 ? B 7DA 123 ? 1_555 157.3 ? 2 N1 ? A 7DA 16 ? A 7DA 116 ? 1_555 AG ? F AG . ? D AG 301 ? 1_555 N3 ? D DT 8 ? D DT 208 ? 1_555 163.4 ? # _pdbx_entry_details.entry_id 9CKH _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 ? _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O2 A DC 120 ? ? N2 D DG 204 ? ? 1.71 2 1 N3 A DC 120 ? ? N1 D DG 204 ? ? 2.08 3 1 O2 A DC 107 ? ? N2 C DG 210 ? ? 2.10 4 1 N6 A 7DA 118 ? ? O4 D DT 206 ? ? 2.19 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 107 ? ? "C1'" A DC 107 ? ? N1 A DC 107 ? ? 111.10 108.30 2.80 0.30 N 2 1 "O4'" A DC 120 ? ? "C1'" A DC 120 ? ? N1 A DC 120 ? ? 110.33 108.30 2.03 0.30 N 3 1 "O4'" D DG 204 ? ? "C1'" D DG 204 ? ? N9 D DG 204 ? ? 110.15 108.30 1.85 0.30 N 4 1 "O4'" D DA 205 ? ? "C1'" D DA 205 ? ? N9 D DA 205 ? ? 110.43 108.30 2.13 0.30 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 x-y,x,z+1/2 3 y,-x+y,z+1/2 4 -y,x-y,z 5 -x+y,-x,z 6 -x,-y,z+1/2 # 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 7DA P P N N 1 7DA OP1 O N N 2 7DA OP2 O N N 3 7DA "O5'" O N N 4 7DA N9 N Y N 5 7DA C4 C Y N 6 7DA N3 N Y N 7 7DA C2 C Y N 8 7DA N1 N Y N 9 7DA C6 C Y N 10 7DA N6 N N N 11 7DA C5 C Y N 12 7DA C7 C Y N 13 7DA C8 C Y N 14 7DA "C2'" C N N 15 7DA "C5'" C N N 16 7DA "C4'" C N R 17 7DA "O4'" O N N 18 7DA "C1'" C N R 19 7DA "C3'" C N S 20 7DA "O3'" O N N 21 7DA OP3 O N N 22 7DA HOP2 H N N 23 7DA H2 H N N 24 7DA HN61 H N N 25 7DA HN62 H N N 26 7DA H7 H N N 27 7DA H8 H N N 28 7DA "H2'" H N N 29 7DA "H2''" H N N 30 7DA "H5'" H N N 31 7DA "H5''" H N N 32 7DA "H4'" H N N 33 7DA "H1'" H N N 34 7DA H1 H N N 35 7DA "HO3'" H N N 36 7DA HOP3 H N N 37 7GU P P N N 38 7GU OP1 O N N 39 7GU OP2 O N N 40 7GU "O5'" O N N 41 7GU N9 N Y N 42 7GU C4 C Y N 43 7GU N3 N N N 44 7GU C2 C N N 45 7GU N2 N N N 46 7GU N1 N N N 47 7GU C6 C N N 48 7GU O6 O N N 49 7GU C5 C Y N 50 7GU C7 C Y N 51 7GU C8 C Y N 52 7GU "C2'" C N N 53 7GU "C5'" C N N 54 7GU "C4'" C N R 55 7GU "O4'" O N N 56 7GU "C1'" C N R 57 7GU "C3'" C N S 58 7GU "O3'" O N N 59 7GU OP3 O N N 60 7GU HOP2 H N N 61 7GU HN21 H N N 62 7GU HN22 H N N 63 7GU HN1 H N N 64 7GU H7 H N N 65 7GU H8 H N N 66 7GU "H2'" H N N 67 7GU "H2''" H N N 68 7GU "H5'" H N N 69 7GU "H5''" H N N 70 7GU "H4'" H N N 71 7GU "H1'" H N N 72 7GU "H3'" H N N 73 7GU "HO3'" H N N 74 7GU HOP3 H N N 75 AG AG AG N N 76 DA OP3 O N N 77 DA P P N N 78 DA OP1 O N N 79 DA OP2 O N N 80 DA "O5'" O N N 81 DA "C5'" C N N 82 DA "C4'" C N R 83 DA "O4'" O N N 84 DA "C3'" C N S 85 DA "O3'" O N N 86 DA "C2'" C N N 87 DA "C1'" C N R 88 DA N9 N Y N 89 DA C8 C Y N 90 DA N7 N Y N 91 DA C5 C Y N 92 DA C6 C Y N 93 DA N6 N N N 94 DA N1 N Y N 95 DA C2 C Y N 96 DA N3 N Y N 97 DA C4 C Y N 98 DA HOP3 H N N 99 DA HOP2 H N N 100 DA "H5'" H N N 101 DA "H5''" H N N 102 DA "H4'" H N N 103 DA "H3'" H N N 104 DA "HO3'" H N N 105 DA "H2'" H N N 106 DA "H2''" H N N 107 DA "H1'" H N N 108 DA H8 H N N 109 DA H61 H N N 110 DA H62 H N N 111 DA H2 H N N 112 DC OP3 O N N 113 DC P P N N 114 DC OP1 O N N 115 DC OP2 O N N 116 DC "O5'" O N N 117 DC "C5'" C N N 118 DC "C4'" C N R 119 DC "O4'" O N N 120 DC "C3'" C N S 121 DC "O3'" O N N 122 DC "C2'" C N N 123 DC "C1'" C N R 124 DC N1 N N N 125 DC C2 C N N 126 DC O2 O N N 127 DC N3 N N N 128 DC C4 C N N 129 DC N4 N N N 130 DC C5 C N N 131 DC C6 C N N 132 DC HOP3 H N N 133 DC HOP2 H N N 134 DC "H5'" H N N 135 DC "H5''" H N N 136 DC "H4'" H N N 137 DC "H3'" H N N 138 DC "HO3'" H N N 139 DC "H2'" H N N 140 DC "H2''" H N N 141 DC "H1'" H N N 142 DC H41 H N N 143 DC H42 H N N 144 DC H5 H N N 145 DC H6 H N N 146 DG OP3 O N N 147 DG P P N N 148 DG OP1 O N N 149 DG OP2 O N N 150 DG "O5'" O N N 151 DG "C5'" C N N 152 DG "C4'" C N R 153 DG "O4'" O N N 154 DG "C3'" C N S 155 DG "O3'" O N N 156 DG "C2'" C N N 157 DG "C1'" C N R 158 DG N9 N Y N 159 DG C8 C Y N 160 DG N7 N Y N 161 DG C5 C Y N 162 DG C6 C N N 163 DG O6 O N N 164 DG N1 N N N 165 DG C2 C N N 166 DG N2 N N N 167 DG N3 N N N 168 DG C4 C Y N 169 DG HOP3 H N N 170 DG HOP2 H N N 171 DG "H5'" H N N 172 DG "H5''" H N N 173 DG "H4'" H N N 174 DG "H3'" H N N 175 DG "HO3'" H N N 176 DG "H2'" H N N 177 DG "H2''" H N N 178 DG "H1'" H N N 179 DG H8 H N N 180 DG H1 H N N 181 DG H21 H N N 182 DG H22 H N N 183 DT OP3 O N N 184 DT P P N N 185 DT OP1 O N N 186 DT OP2 O N N 187 DT "O5'" O N N 188 DT "C5'" C N N 189 DT "C4'" C N R 190 DT "O4'" O N N 191 DT "C3'" C N S 192 DT "O3'" O N N 193 DT "C2'" C N N 194 DT "C1'" C N R 195 DT N1 N N N 196 DT C2 C N N 197 DT O2 O N N 198 DT N3 N N N 199 DT C4 C N N 200 DT O4 O N N 201 DT C5 C N N 202 DT C7 C N N 203 DT C6 C N N 204 DT HOP3 H N N 205 DT HOP2 H N N 206 DT "H5'" H N N 207 DT "H5''" H N N 208 DT "H4'" H N N 209 DT "H3'" H N N 210 DT "HO3'" H N N 211 DT "H2'" H N N 212 DT "H2''" H N N 213 DT "H1'" H N N 214 DT H3 H N N 215 DT H71 H N N 216 DT H72 H N N 217 DT H73 H N N 218 DT H6 H N N 219 # 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 7DA P OP1 doub N N 1 7DA P OP2 sing N N 2 7DA P "O5'" sing N N 3 7DA P OP3 sing N N 4 7DA OP2 HOP2 sing N N 5 7DA "O5'" "C5'" sing N N 6 7DA N9 C4 sing Y N 7 7DA N9 C8 sing Y N 8 7DA N9 "C1'" sing N N 9 7DA C4 N3 sing Y N 10 7DA C4 C5 doub Y N 11 7DA N3 C2 doub Y N 12 7DA C2 N1 sing Y N 13 7DA C2 H2 sing N N 14 7DA N1 C6 doub Y N 15 7DA C6 N6 sing N N 16 7DA C6 C5 sing Y N 17 7DA N6 HN61 sing N N 18 7DA N6 HN62 sing N N 19 7DA C5 C7 sing Y N 20 7DA C7 C8 doub Y N 21 7DA C7 H7 sing N N 22 7DA C8 H8 sing N N 23 7DA "C2'" "C1'" sing N N 24 7DA "C2'" "C3'" sing N N 25 7DA "C2'" "H2'" sing N N 26 7DA "C2'" "H2''" sing N N 27 7DA "C5'" "C4'" sing N N 28 7DA "C5'" "H5'" sing N N 29 7DA "C5'" "H5''" sing N N 30 7DA "C4'" "O4'" sing N N 31 7DA "C4'" "C3'" sing N N 32 7DA "C4'" "H4'" sing N N 33 7DA "O4'" "C1'" sing N N 34 7DA "C1'" "H1'" sing N N 35 7DA "C3'" "O3'" sing N N 36 7DA "C3'" H1 sing N N 37 7DA "O3'" "HO3'" sing N N 38 7DA OP3 HOP3 sing N N 39 7GU P OP1 doub N N 40 7GU P OP2 sing N N 41 7GU P "O5'" sing N N 42 7GU P OP3 sing N N 43 7GU OP2 HOP2 sing N N 44 7GU "O5'" "C5'" sing N N 45 7GU N9 C4 sing Y N 46 7GU N9 C8 sing Y N 47 7GU N9 "C1'" sing N N 48 7GU C4 N3 sing N N 49 7GU C4 C5 doub Y N 50 7GU N3 C2 doub N N 51 7GU C2 N2 sing N N 52 7GU C2 N1 sing N N 53 7GU N2 HN21 sing N N 54 7GU N2 HN22 sing N N 55 7GU N1 C6 sing N N 56 7GU N1 HN1 sing N N 57 7GU C6 O6 doub N N 58 7GU C6 C5 sing N N 59 7GU C5 C7 sing Y N 60 7GU C7 C8 doub Y N 61 7GU C7 H7 sing N N 62 7GU C8 H8 sing N N 63 7GU "C2'" "C1'" sing N N 64 7GU "C2'" "C3'" sing N N 65 7GU "C2'" "H2'" sing N N 66 7GU "C2'" "H2''" sing N N 67 7GU "C5'" "C4'" sing N N 68 7GU "C5'" "H5'" sing N N 69 7GU "C5'" "H5''" sing N N 70 7GU "C4'" "O4'" sing N N 71 7GU "C4'" "C3'" sing N N 72 7GU "C4'" "H4'" sing N N 73 7GU "O4'" "C1'" sing N N 74 7GU "C1'" "H1'" sing N N 75 7GU "C3'" "O3'" sing N N 76 7GU "C3'" "H3'" sing N N 77 7GU "O3'" "HO3'" sing N N 78 7GU OP3 HOP3 sing N N 79 DA OP3 P sing N N 80 DA OP3 HOP3 sing N N 81 DA P OP1 doub N N 82 DA P OP2 sing N N 83 DA P "O5'" sing N N 84 DA OP2 HOP2 sing N N 85 DA "O5'" "C5'" sing N N 86 DA "C5'" "C4'" sing N N 87 DA "C5'" "H5'" sing N N 88 DA "C5'" "H5''" sing N N 89 DA "C4'" "O4'" sing N N 90 DA "C4'" "C3'" sing N N 91 DA "C4'" "H4'" sing N N 92 DA "O4'" "C1'" sing N N 93 DA "C3'" "O3'" sing N N 94 DA "C3'" "C2'" sing N N 95 DA "C3'" "H3'" sing N N 96 DA "O3'" "HO3'" sing N N 97 DA "C2'" "C1'" sing N N 98 DA "C2'" "H2'" sing N N 99 DA "C2'" "H2''" sing N N 100 DA "C1'" N9 sing N N 101 DA "C1'" "H1'" sing N N 102 DA N9 C8 sing Y N 103 DA N9 C4 sing Y N 104 DA C8 N7 doub Y N 105 DA C8 H8 sing N N 106 DA N7 C5 sing Y N 107 DA C5 C6 sing Y N 108 DA C5 C4 doub Y N 109 DA C6 N6 sing N N 110 DA C6 N1 doub Y N 111 DA N6 H61 sing N N 112 DA N6 H62 sing N N 113 DA N1 C2 sing Y N 114 DA C2 N3 doub Y N 115 DA C2 H2 sing N N 116 DA N3 C4 sing Y N 117 DC OP3 P sing N N 118 DC OP3 HOP3 sing N N 119 DC P OP1 doub N N 120 DC P OP2 sing N N 121 DC P "O5'" sing N N 122 DC OP2 HOP2 sing N N 123 DC "O5'" "C5'" sing N N 124 DC "C5'" "C4'" sing N N 125 DC "C5'" "H5'" sing N N 126 DC "C5'" "H5''" sing N N 127 DC "C4'" "O4'" sing N N 128 DC "C4'" "C3'" sing N N 129 DC "C4'" "H4'" sing N N 130 DC "O4'" "C1'" sing N N 131 DC "C3'" "O3'" sing N N 132 DC "C3'" "C2'" sing N N 133 DC "C3'" "H3'" sing N N 134 DC "O3'" "HO3'" sing N N 135 DC "C2'" "C1'" sing N N 136 DC "C2'" "H2'" sing N N 137 DC "C2'" "H2''" sing N N 138 DC "C1'" N1 sing N N 139 DC "C1'" "H1'" sing N N 140 DC N1 C2 sing N N 141 DC N1 C6 sing N N 142 DC C2 O2 doub N N 143 DC C2 N3 sing N N 144 DC N3 C4 doub N N 145 DC C4 N4 sing N N 146 DC C4 C5 sing N N 147 DC N4 H41 sing N N 148 DC N4 H42 sing N N 149 DC C5 C6 doub N N 150 DC C5 H5 sing N N 151 DC C6 H6 sing N N 152 DG OP3 P sing N N 153 DG OP3 HOP3 sing N N 154 DG P OP1 doub N N 155 DG P OP2 sing N N 156 DG P "O5'" sing N N 157 DG OP2 HOP2 sing N N 158 DG "O5'" "C5'" sing N N 159 DG "C5'" "C4'" sing N N 160 DG "C5'" "H5'" sing N N 161 DG "C5'" "H5''" sing N N 162 DG "C4'" "O4'" sing N N 163 DG "C4'" "C3'" sing N N 164 DG "C4'" "H4'" sing N N 165 DG "O4'" "C1'" sing N N 166 DG "C3'" "O3'" sing N N 167 DG "C3'" "C2'" sing N N 168 DG "C3'" "H3'" sing N N 169 DG "O3'" "HO3'" sing N N 170 DG "C2'" "C1'" sing N N 171 DG "C2'" "H2'" sing N N 172 DG "C2'" "H2''" sing N N 173 DG "C1'" N9 sing N N 174 DG "C1'" "H1'" sing N N 175 DG N9 C8 sing Y N 176 DG N9 C4 sing Y N 177 DG C8 N7 doub Y N 178 DG C8 H8 sing N N 179 DG N7 C5 sing Y N 180 DG C5 C6 sing N N 181 DG C5 C4 doub Y N 182 DG C6 O6 doub N N 183 DG C6 N1 sing N N 184 DG N1 C2 sing N N 185 DG N1 H1 sing N N 186 DG C2 N2 sing N N 187 DG C2 N3 doub N N 188 DG N2 H21 sing N N 189 DG N2 H22 sing N N 190 DG N3 C4 sing N N 191 DT OP3 P sing N N 192 DT OP3 HOP3 sing N N 193 DT P OP1 doub N N 194 DT P OP2 sing N N 195 DT P "O5'" sing N N 196 DT OP2 HOP2 sing N N 197 DT "O5'" "C5'" sing N N 198 DT "C5'" "C4'" sing N N 199 DT "C5'" "H5'" sing N N 200 DT "C5'" "H5''" sing N N 201 DT "C4'" "O4'" sing N N 202 DT "C4'" "C3'" sing N N 203 DT "C4'" "H4'" sing N N 204 DT "O4'" "C1'" sing N N 205 DT "C3'" "O3'" sing N N 206 DT "C3'" "C2'" sing N N 207 DT "C3'" "H3'" sing N N 208 DT "O3'" "HO3'" sing N N 209 DT "C2'" "C1'" sing N N 210 DT "C2'" "H2'" sing N N 211 DT "C2'" "H2''" sing N N 212 DT "C1'" N1 sing N N 213 DT "C1'" "H1'" sing N N 214 DT N1 C2 sing N N 215 DT N1 C6 sing N N 216 DT C2 O2 doub N N 217 DT C2 N3 sing N N 218 DT N3 C4 sing N N 219 DT N3 H3 sing N N 220 DT C4 O4 doub N N 221 DT C4 C5 sing N N 222 DT C5 C7 sing N N 223 DT C5 C6 doub N N 224 DT C7 H71 sing N N 225 DT C7 H72 sing N N 226 DT C7 H73 sing N N 227 DT C6 H6 sing N N 228 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9CKH 'double helix' 9CKH 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A 7GU 3 1_555 C DC 6 1_555 0.030 -0.667 0.820 8.783 -6.062 -3.188 1 A_7GU103:DC214_C A 103 ? C 214 ? 19 1 1 A DC 4 1_555 C DG 5 1_555 0.126 -0.155 -0.039 3.917 -4.298 -0.490 2 A_DC104:DG213_C A 104 ? C 213 ? 19 1 1 A 7DA 5 1_555 C DT 4 1_555 0.525 -0.038 -0.147 -0.893 -6.023 -16.720 3 A_7DA105:DT212_C A 105 ? C 212 ? 20 1 1 A 7GU 6 1_555 C DC 3 1_555 -0.169 -0.166 -0.447 0.259 -3.830 -1.170 4 A_7GU106:DC211_C A 106 ? C 211 ? 19 1 1 A DC 7 1_555 C DG 2 1_555 0.112 -0.645 0.045 5.741 -6.483 3.616 5 A_DC107:DG210_C A 107 ? C 210 ? 22 1 1 A DC 8 1_555 C DG 1 1_555 -0.059 -0.617 0.260 1.201 -7.910 -3.114 6 A_DC108:DG209_C A 108 ? C 209 ? 19 1 1 A DT 9 1_555 B 7DA 7 1_555 -0.981 -0.021 0.218 -3.201 0.116 -14.191 7 A_DT109:7DA125_B A 109 ? B 125 ? 20 1 1 A 7GU 10 1_555 B DC 6 1_555 -0.158 0.108 -0.062 4.278 4.025 -1.211 8 A_7GU110:DC124_B A 110 ? B 124 ? 19 1 1 A 7DA 12 1_555 B DT 4 1_555 0.180 -0.381 0.243 -1.878 -1.953 0.123 9 A_7DA112:DT122_B A 112 ? B 122 ? 20 1 1 A DC 13 1_555 B 7GU 3 1_555 0.092 0.118 0.033 3.573 -6.662 -8.774 10 A_DC113:7GU121_B A 113 ? B 121 ? 19 1 1 A 7GU 14 1_555 B DC 2 1_555 -0.206 0.084 0.331 0.229 -8.083 -9.408 11 A_7GU114:DC120_B A 114 ? B 120 ? 19 1 1 A 7GU 15 1_555 B DC 1 1_555 -0.204 0.379 0.048 1.775 -9.568 -0.416 12 A_7GU115:DC119_B A 115 ? B 119 ? 19 1 1 A DC 17 1_555 D DG 7 1_555 0.280 0.189 0.589 -7.010 -10.085 2.428 13 A_DC117:DG207_D A 117 ? D 207 ? 19 1 1 A 7DA 18 1_555 D DT 6 1_555 0.713 -0.349 0.208 -2.851 -6.988 -9.749 14 A_7DA118:DT206_D A 118 ? D 206 ? ? 1 1 A DT 19 1_555 D DA 5 1_555 0.005 -0.690 0.119 1.971 -1.890 5.694 15 A_DT119:DA205_D A 119 ? D 205 ? 20 1 1 A DC 20 1_555 D DG 4 1_555 0.092 -0.845 -0.084 3.663 -5.353 8.013 16 A_DC120:DG204_D A 120 ? D 204 ? 22 1 1 A 7DA 21 1_555 D DT 3 1_555 -0.041 -0.476 0.009 -0.267 -3.963 7.628 17 A_7DA121:DT203_D A 121 ? D 203 ? 20 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 7GU 3 1_555 C DC 6 1_555 A DC 4 1_555 C DG 5 1_555 0.222 -1.579 3.385 4.539 -0.517 36.978 -2.401 0.280 3.409 -0.812 -7.122 37.249 1 AA_7GU103DC104:DG213DC214_CC A 103 ? C 214 ? A 104 ? C 213 ? 1 A DC 4 1_555 C DG 5 1_555 A 7DA 5 1_555 C DT 4 1_555 -1.701 -0.478 3.463 -1.876 -5.157 31.430 0.149 2.725 3.587 -9.430 3.431 31.893 2 AA_DC1047DA105:DT212DG213_CC A 104 ? C 213 ? A 105 ? C 212 ? 1 A 7DA 5 1_555 C DT 4 1_555 A 7GU 6 1_555 C DC 3 1_555 1.256 0.213 3.912 -0.002 -1.417 31.280 0.715 -2.329 3.899 -2.626 0.004 31.311 3 AA_7DA1057GU106:DC211DT212_CC A 105 ? C 212 ? A 106 ? C 211 ? 1 A 7GU 6 1_555 C DC 3 1_555 A DC 7 1_555 C DG 2 1_555 1.332 -0.555 2.945 -0.993 -0.147 34.305 -0.920 -2.397 2.908 -0.250 1.683 34.319 4 AA_7GU106DC107:DG210DC211_CC A 106 ? C 211 ? A 107 ? C 210 ? 1 A DC 7 1_555 C DG 2 1_555 A DC 8 1_555 C DG 1 1_555 -0.616 -0.693 2.968 -3.735 1.689 40.500 -1.167 0.508 2.981 2.432 5.379 40.698 5 AA_DC107DC108:DG209DG210_CC A 107 ? C 210 ? A 108 ? C 209 ? 1 A DC 8 1_555 C DG 1 1_555 A DT 9 1_555 B 7DA 7 1_555 -1.958 -1.660 3.263 0.375 7.061 22.565 -6.210 4.895 2.597 17.502 -0.929 23.633 6 AA_DC108DT109:7DA125DG209_BC A 108 ? C 209 ? A 109 ? B 125 ? 1 A DT 9 1_555 B 7DA 7 1_555 A 7GU 10 1_555 B DC 6 1_555 0.849 -0.641 3.547 -4.557 4.276 35.065 -1.707 -2.090 3.316 7.028 7.489 35.600 7 AA_DT1097GU110:DC1247DA125_BB A 109 ? B 125 ? A 110 ? B 124 ? 1 A 7DA 12 1_555 B DT 4 1_555 A DC 13 1_555 B 7GU 3 1_555 -1.097 0.314 2.897 2.699 -0.405 36.529 0.549 2.068 2.808 -0.645 -4.299 36.628 8 AA_7DA112DC113:7GU121DT122_BB A 112 ? B 122 ? A 113 ? B 121 ? 1 A DC 13 1_555 B 7GU 3 1_555 A 7GU 14 1_555 B DC 2 1_555 -0.217 2.894 3.296 0.821 -2.606 41.282 4.370 0.393 3.111 -3.692 -1.163 41.368 9 AA_DC1137GU114:DC1207GU121_BB A 113 ? B 121 ? A 114 ? B 120 ? 1 A 7GU 14 1_555 B DC 2 1_555 A 7GU 15 1_555 B DC 1 1_555 0.835 0.007 3.171 -0.365 -1.911 37.043 0.258 -1.361 3.159 -3.006 0.575 37.092 10 AA_7GU1147GU115:DC119DC120_BB A 114 ? B 120 ? A 115 ? B 119 ? 1 A DC 17 1_555 D DG 7 1_555 A 7DA 18 1_555 D DT 6 1_555 -0.826 0.032 2.777 3.251 5.569 33.663 -0.680 1.831 2.659 9.507 -5.550 34.258 11 AA_DC1177DA118:DT206DG207_DD A 117 ? D 207 ? A 118 ? D 206 ? 1 A 7DA 18 1_555 D DT 6 1_555 A DT 19 1_555 D DA 5 1_555 1.430 -0.577 2.960 3.060 1.458 28.065 -1.495 -2.271 3.062 2.992 -6.281 28.265 12 AA_7DA118DT119:DA205DT206_DD A 118 ? D 206 ? A 119 ? D 205 ? 1 A DT 19 1_555 D DA 5 1_555 A DC 20 1_555 D DG 4 1_555 1.079 0.026 2.913 3.069 0.549 31.233 -0.046 -1.472 3.002 1.017 -5.683 31.384 13 AA_DT119DC120:DG204DA205_DD A 119 ? D 205 ? A 120 ? D 204 ? 1 A DC 20 1_555 D DG 4 1_555 A 7DA 21 1_555 D DT 3 1_555 0.043 -0.654 3.204 0.276 8.129 30.868 -2.603 -0.031 2.941 14.950 -0.508 31.896 14 AA_DC1207DA121:DT203DG204_DD A 120 ? D 204 ? A 121 ? D 203 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Office of Naval Research (ONR)' 'United States' N000141912596 1 'National Science Foundation (NSF, United States)' 'United States' CCF-2106790 2 'National Science Foundation (NSF, United States)' 'United States' GCR-2317843 3 'Department of Energy (DOE, United States)' 'United States' DE-SC0007991 4 # _space_group.name_H-M_alt 'P 63' _space_group.name_Hall 'P 6c' _space_group.IT_number 173 _space_group.crystal_system hexagonal _space_group.id 1 # _atom_sites.entry_id 9CKH _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.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.008112 _atom_sites.fract_transf_matrix[1][2] 0.004683 _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] 0.009367 _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] 0.016060 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source AG ? ? 46.70359 ? ? ? 5.43095 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? C ? ? 5.96793 ? ? ? 14.89577 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 6.96715 ? ? ? 11.43723 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 7.96527 ? ? ? 9.05267 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 14.90797 ? ? ? 11.91318 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ #