data_1Y9F # _entry.id 1Y9F # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1Y9F pdb_00001y9f 10.2210/pdb1y9f/pdb NDB AD0039 ? ? RCSB RCSB031282 ? ? WWPDB D_1000031282 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1Y7F ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy(methyleneamino)oxy]ethyl] Thymidine (T*) ; unspecified PDB 1Y84 ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(imidazolyl)ethyl] Thymidine (T*) ; unspecified PDB 1Y86 ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(fluoro)ethyl] Thymidine (T*) ; unspecified PDB 1Y8L ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(trifluoro)ethyl] Thymidine (T*) ; unspecified PDB 1Y8V ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thymidine (T*) ; unspecified PDB 1Y9S ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propargyl Thymidine (T*) ; unspecified PDB 1WV5 ;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL THYMINE IN PLACE OF T6, MG-FORM ; unspecified PDB 1WV6 ;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL THYMINE IN PLACE OF T6, SR-FORM ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Y9F _pdbx_database_status.recvd_initial_deposition_date 2004-12-15 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Egli, M.' 1 'Minasov, G.' 2 'Tereshko, V.' 3 'Pallan, P.S.' 4 'Teplova, M.' 5 'Inamati, G.B.' 6 'Lesnik, E.A.' 7 'Owens, S.R.' 8 'Ross, B.S.' 9 'Prakash, T.P.' 10 'Manoharan, M.' 11 # _citation.id primary _citation.title ;Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 44 _citation.page_first 9045 _citation.page_last 9057 _citation.year 2005 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15966728 _citation.pdbx_database_id_DOI 10.1021/bi050574m # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Egli, M.' 1 ? primary 'Minasov, G.' 2 ? primary 'Tereshko, V.' 3 ? primary 'Pallan, P.S.' 4 ? primary 'Teplova, M.' 5 ? primary 'Inamati, G.B.' 6 ? primary 'Lesnik, E.A.' 7 ? primary 'Owens, S.R.' 8 ? primary 'Ross, B.S.' 9 ? primary 'Prakash, T.P.' 10 ? primary 'Manoharan, M.' 11 ? # _cell.entry_id 1Y9F _cell.length_a 24.696 _cell.length_b 45.070 _cell.length_c 45.640 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y9F _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*GP*CP*GP*TP*AP*(2AT)P*AP*CP*GP*C)-3')" 3101.069 2 ? ? ? ? 2 water nat water 18.015 127 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(DT)(DA)(2AT)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTATACGC _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 DG n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 2AT n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1Y9F _struct_ref.pdbx_db_accession 1Y9F _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1Y9F A 1 ? 10 ? 1Y9F 1 ? 10 ? 1 10 2 1 1Y9F B 1 ? 10 ? 1Y9F 11 ? 20 ? 11 20 # 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 2AT 'RNA linking' n ;2'-O-ALLYL THYMIDINE-5'-MONOPHOSPHATE ; ? 'C13 H19 N2 O9 P' 378.272 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 1Y9F _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.05 _exptl_crystal.density_percent_sol 39.93 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details '10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM KCL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 Na-Cacodilate ? ? ? 1 3 1 Spermine ? ? ? 1 4 1 KCL ? ? ? 1 5 1 H2O ? ? ? 1 6 2 MPD ? ? ? 1 7 2 Na-Cacodilate ? ? ? 1 8 2 KCL ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date 1998-07-17 _diffrn_detector.details Mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1Y9F _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3.0 _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 35.00 _reflns.number_all 6760 _reflns.number_obs 6760 _reflns.percent_possible_obs 94.1 _reflns.pdbx_Rmerge_I_obs 0.071 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 25.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.2 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.66 _reflns_shell.percent_possible_all 77.9 _reflns_shell.Rmerge_I_obs 0.222 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.3 _reflns_shell.pdbx_redundancy 2.4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 549 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1Y9F _refine.ls_d_res_high 1.60 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 6528 _refine.ls_number_reflns_obs 6528 _refine.ls_number_reflns_R_free 712 _refine.ls_percent_reflns_obs 91.5 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1583 _refine.ls_R_factor_R_free 0.1852 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'pdb entry 410D' _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details Random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model Isotropic _refine.B_iso_mean 18.4 _refine.aniso_B[1][1] 1.586 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][2] -4.721 _refine.aniso_B[2][3] 0.000 _refine.aniso_B[3][3] 3.135 _refine.details 'Conjugate gradient refinement using maximum likelihood target for amplitudes' _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 412 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 131 _refine_hist.number_atoms_total 543 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 20.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.32 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.60 _refine_ls_shell.d_res_low 1.64 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.2449 _refine_ls_shell.percent_reflns_obs 55.3 _refine_ls_shell.R_factor_R_free 0.2706 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 39 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1Y9F _struct.title ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-allyl Thymidine (T*) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Y9F _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;A-DNA, O2'-modification, decamer, DNA ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_biol.id 1 _struct_biol.details 'Chains A and B form duplex' _struct_biol.pdbx_parent_biol_id ? # 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 5 "O3'" ? ? ? 1_555 A 2AT 6 P ? ? A DA 5 A 2AT 6 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale2 covale both ? A 2AT 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A 2AT 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B 2AT 6 P ? ? B DA 15 B 2AT 16 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale4 covale both ? B 2AT 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B 2AT 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.592 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B 2AT 6 N3 ? ? A DA 5 B 2AT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B 2AT 6 O4 ? ? A DA 5 B 2AT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 2AT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A 2AT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 2AT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A 2AT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1Y9F _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1Y9F _atom_sites.fract_transf_matrix[1][1] 0.040492 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022188 _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] 0.021911 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 2AT 6 6 6 2AT ALY A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n B 1 1 DG 1 11 11 DG G B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 2AT 6 16 16 2AT ALY B . n B 1 7 DA 7 17 17 DA A B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DC 10 20 20 DC C 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 HOH 1 101 101 HOH HOH A . C 2 HOH 2 102 102 HOH HOH A . C 2 HOH 3 103 103 HOH HOH A . C 2 HOH 4 106 106 HOH HOH A . C 2 HOH 5 107 107 HOH HOH A . C 2 HOH 6 108 108 HOH HOH A . C 2 HOH 7 109 109 HOH HOH A . C 2 HOH 8 110 110 HOH HOH A . C 2 HOH 9 111 111 HOH HOH A . C 2 HOH 10 112 112 HOH HOH A . C 2 HOH 11 114 114 HOH HOH A . C 2 HOH 12 115 115 HOH HOH A . C 2 HOH 13 117 117 HOH HOH A . C 2 HOH 14 118 118 HOH HOH A . C 2 HOH 15 120 120 HOH HOH A . C 2 HOH 16 122 122 HOH HOH A . C 2 HOH 17 123 123 HOH HOH A . C 2 HOH 18 124 124 HOH HOH A . C 2 HOH 19 126 126 HOH HOH A . C 2 HOH 20 130 130 HOH HOH A . C 2 HOH 21 131 131 HOH HOH A . C 2 HOH 22 134 134 HOH HOH A . C 2 HOH 23 135 135 HOH HOH A . C 2 HOH 24 137 137 HOH HOH A . C 2 HOH 25 141 141 HOH HOH A . C 2 HOH 26 143 143 HOH HOH A . C 2 HOH 27 144 144 HOH HOH A . C 2 HOH 28 145 145 HOH HOH A . C 2 HOH 29 147 147 HOH HOH A . C 2 HOH 30 148 148 HOH HOH A . C 2 HOH 31 149 149 HOH HOH A . C 2 HOH 32 150 150 HOH HOH A . C 2 HOH 33 151 151 HOH HOH A . C 2 HOH 34 152 152 HOH HOH A . C 2 HOH 35 155 155 HOH HOH A . C 2 HOH 36 156 156 HOH HOH A . C 2 HOH 37 159 159 HOH HOH A . C 2 HOH 38 160 160 HOH HOH A . C 2 HOH 39 161 161 HOH HOH A . C 2 HOH 40 162 162 HOH HOH A . C 2 HOH 41 163 163 HOH HOH A . C 2 HOH 42 164 164 HOH HOH A . C 2 HOH 43 166 166 HOH HOH A . C 2 HOH 44 168 168 HOH HOH A . C 2 HOH 45 170 170 HOH HOH A . C 2 HOH 46 173 173 HOH HOH A . C 2 HOH 47 175 175 HOH HOH A . C 2 HOH 48 176 176 HOH HOH A . C 2 HOH 49 178 178 HOH HOH A . C 2 HOH 50 180 180 HOH HOH A . C 2 HOH 51 185 185 HOH HOH A . C 2 HOH 52 186 186 HOH HOH A . C 2 HOH 53 187 187 HOH HOH A . C 2 HOH 54 188 188 HOH HOH A . C 2 HOH 55 190 190 HOH HOH A . C 2 HOH 56 191 191 HOH HOH A . C 2 HOH 57 195 195 HOH HOH A . C 2 HOH 58 196 196 HOH HOH A . C 2 HOH 59 197 197 HOH HOH A . C 2 HOH 60 198 198 HOH HOH A . C 2 HOH 61 199 199 HOH HOH A . C 2 HOH 62 200 200 HOH HOH A . C 2 HOH 63 201 201 HOH HOH A . C 2 HOH 64 203 203 HOH HOH A . C 2 HOH 65 204 204 HOH HOH A . C 2 HOH 66 207 207 HOH HOH A . C 2 HOH 67 208 208 HOH HOH A . C 2 HOH 68 209 209 HOH HOH A . C 2 HOH 69 210 210 HOH HOH A . C 2 HOH 70 211 211 HOH HOH A . C 2 HOH 71 212 212 HOH HOH A . C 2 HOH 72 213 213 HOH HOH A . C 2 HOH 73 214 214 HOH HOH A . C 2 HOH 74 215 215 HOH HOH A . C 2 HOH 75 217 217 HOH HOH A . C 2 HOH 76 218 218 HOH HOH A . C 2 HOH 77 220 220 HOH HOH A . C 2 HOH 78 223 223 HOH HOH A . C 2 HOH 79 224 224 HOH HOH A . C 2 HOH 80 225 225 HOH HOH A . C 2 HOH 81 227 227 HOH HOH A . D 2 HOH 1 104 104 HOH HOH B . D 2 HOH 2 105 105 HOH HOH B . D 2 HOH 3 113 113 HOH HOH B . D 2 HOH 4 116 116 HOH HOH B . D 2 HOH 5 119 119 HOH HOH B . D 2 HOH 6 121 121 HOH HOH B . D 2 HOH 7 125 125 HOH HOH B . D 2 HOH 8 127 127 HOH HOH B . D 2 HOH 9 128 128 HOH HOH B . D 2 HOH 10 129 129 HOH HOH B . D 2 HOH 11 132 132 HOH HOH B . D 2 HOH 12 133 133 HOH HOH B . D 2 HOH 13 136 136 HOH HOH B . D 2 HOH 14 138 138 HOH HOH B . D 2 HOH 15 139 139 HOH HOH B . D 2 HOH 16 140 140 HOH HOH B . D 2 HOH 17 142 142 HOH HOH B . D 2 HOH 18 146 146 HOH HOH B . D 2 HOH 19 153 153 HOH HOH B . D 2 HOH 20 154 154 HOH HOH B . D 2 HOH 21 157 157 HOH HOH B . D 2 HOH 22 158 158 HOH HOH B . D 2 HOH 23 165 165 HOH HOH B . D 2 HOH 24 167 167 HOH HOH B . D 2 HOH 25 169 169 HOH HOH B . D 2 HOH 26 171 171 HOH HOH B . D 2 HOH 27 172 172 HOH HOH B . D 2 HOH 28 174 174 HOH HOH B . D 2 HOH 29 177 177 HOH HOH B . D 2 HOH 30 179 179 HOH HOH B . D 2 HOH 31 181 181 HOH HOH B . D 2 HOH 32 182 182 HOH HOH B . D 2 HOH 33 183 183 HOH HOH B . D 2 HOH 34 184 184 HOH HOH B . D 2 HOH 35 189 189 HOH HOH B . D 2 HOH 36 192 192 HOH HOH B . D 2 HOH 37 193 193 HOH HOH B . D 2 HOH 38 194 194 HOH HOH B . D 2 HOH 39 202 202 HOH HOH B . D 2 HOH 40 205 205 HOH HOH B . D 2 HOH 41 206 206 HOH HOH B . D 2 HOH 42 216 216 HOH HOH B . D 2 HOH 43 219 219 HOH HOH B . D 2 HOH 44 221 221 HOH HOH B . D 2 HOH 45 222 222 HOH HOH B . D 2 HOH 46 226 226 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 2AT 6 A 2AT 6 ? DT ;2'-O-ALLYL THYMIDINE-5'-MONOPHOSPHATE ; 2 B 2AT 6 B 2AT 16 ? DT ;2'-O-ALLYL THYMIDINE-5'-MONOPHOSPHATE ; # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2005-06-28 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-23 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' struct_conn # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement . ? 4 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DG B 19 ? ? 0.075 'SIDE CHAIN' 2 1 DC B 20 ? ? 0.065 'SIDE CHAIN' # 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 2AT P P N N 1 2AT OP1 O N N 2 2AT OP2 O N N 3 2AT "O5'" O N N 4 2AT "C5'" C N N 5 2AT "C4'" C N R 6 2AT "O4'" O N N 7 2AT "C1'" C N R 8 2AT N1 N N N 9 2AT C6 C N N 10 2AT C2 C N N 11 2AT O2 O N N 12 2AT N3 N N N 13 2AT C4 C N N 14 2AT O4 O N N 15 2AT C5 C N N 16 2AT C5M C N N 17 2AT "C2'" C N R 18 2AT "O2'" O N N 19 2AT "CB'" C N N 20 2AT "CC'" C N N 21 2AT "CD'" C N N 22 2AT "C3'" C N R 23 2AT "O3'" O N N 24 2AT OP3 O N N 25 2AT HOP2 H N N 26 2AT "H5'" H N N 27 2AT "H5''" H N N 28 2AT "H4'" H N N 29 2AT "H1'" H N N 30 2AT H6 H N N 31 2AT HN3 H N N 32 2AT H71 H N N 33 2AT H72 H N N 34 2AT H73 H N N 35 2AT "H2'" H N N 36 2AT "HB'1" H N N 37 2AT "HB'2" H N N 38 2AT "HC'" H N N 39 2AT "HD'1" H N N 40 2AT "HD'2" H N N 41 2AT "H3'" H N N 42 2AT "HO3'" H N N 43 2AT HOP3 H N N 44 DA OP3 O N N 45 DA P P N N 46 DA OP1 O N N 47 DA OP2 O N N 48 DA "O5'" O N N 49 DA "C5'" C N N 50 DA "C4'" C N R 51 DA "O4'" O N N 52 DA "C3'" C N S 53 DA "O3'" O N N 54 DA "C2'" C N N 55 DA "C1'" C N R 56 DA N9 N Y N 57 DA C8 C Y N 58 DA N7 N Y N 59 DA C5 C Y N 60 DA C6 C Y N 61 DA N6 N N N 62 DA N1 N Y N 63 DA C2 C Y N 64 DA N3 N Y N 65 DA C4 C Y N 66 DA HOP3 H N N 67 DA HOP2 H N N 68 DA "H5'" H N N 69 DA "H5''" H N N 70 DA "H4'" H N N 71 DA "H3'" H N N 72 DA "HO3'" H N N 73 DA "H2'" H N N 74 DA "H2''" H N N 75 DA "H1'" H N N 76 DA H8 H N N 77 DA H61 H N N 78 DA H62 H N N 79 DA H2 H N N 80 DC OP3 O N N 81 DC P P N N 82 DC OP1 O N N 83 DC OP2 O N N 84 DC "O5'" O N N 85 DC "C5'" C N N 86 DC "C4'" C N R 87 DC "O4'" O N N 88 DC "C3'" C N S 89 DC "O3'" O N N 90 DC "C2'" C N N 91 DC "C1'" C N R 92 DC N1 N N N 93 DC C2 C N N 94 DC O2 O N N 95 DC N3 N N N 96 DC C4 C N N 97 DC N4 N N N 98 DC C5 C N N 99 DC C6 C N N 100 DC HOP3 H N N 101 DC HOP2 H N N 102 DC "H5'" H N N 103 DC "H5''" H N N 104 DC "H4'" H N N 105 DC "H3'" H N N 106 DC "HO3'" H N N 107 DC "H2'" H N N 108 DC "H2''" H N N 109 DC "H1'" H N N 110 DC H41 H N N 111 DC H42 H N N 112 DC H5 H N N 113 DC H6 H N N 114 DG OP3 O N N 115 DG P P N N 116 DG OP1 O N N 117 DG OP2 O N N 118 DG "O5'" O N N 119 DG "C5'" C N N 120 DG "C4'" C N R 121 DG "O4'" O N N 122 DG "C3'" C N S 123 DG "O3'" O N N 124 DG "C2'" C N N 125 DG "C1'" C N R 126 DG N9 N Y N 127 DG C8 C Y N 128 DG N7 N Y N 129 DG C5 C Y N 130 DG C6 C N N 131 DG O6 O N N 132 DG N1 N N N 133 DG C2 C N N 134 DG N2 N N N 135 DG N3 N N N 136 DG C4 C Y N 137 DG HOP3 H N N 138 DG HOP2 H N N 139 DG "H5'" H N N 140 DG "H5''" H N N 141 DG "H4'" H N N 142 DG "H3'" H N N 143 DG "HO3'" H N N 144 DG "H2'" H N N 145 DG "H2''" H N N 146 DG "H1'" H N N 147 DG H8 H N N 148 DG H1 H N N 149 DG H21 H N N 150 DG H22 H N N 151 DT OP3 O N N 152 DT P P N N 153 DT OP1 O N N 154 DT OP2 O N N 155 DT "O5'" O N N 156 DT "C5'" C N N 157 DT "C4'" C N R 158 DT "O4'" O N N 159 DT "C3'" C N S 160 DT "O3'" O N N 161 DT "C2'" C N N 162 DT "C1'" C N R 163 DT N1 N N N 164 DT C2 C N N 165 DT O2 O N N 166 DT N3 N N N 167 DT C4 C N N 168 DT O4 O N N 169 DT C5 C N N 170 DT C7 C N N 171 DT C6 C N N 172 DT HOP3 H N N 173 DT HOP2 H N N 174 DT "H5'" H N N 175 DT "H5''" H N N 176 DT "H4'" H N N 177 DT "H3'" H N N 178 DT "HO3'" H N N 179 DT "H2'" H N N 180 DT "H2''" H N N 181 DT "H1'" H N N 182 DT H3 H N N 183 DT H71 H N N 184 DT H72 H N N 185 DT H73 H N N 186 DT H6 H N N 187 HOH O O N N 188 HOH H1 H N N 189 HOH H2 H N N 190 # 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 2AT P OP1 doub N N 1 2AT P OP2 sing N N 2 2AT P "O5'" sing N N 3 2AT P OP3 sing N N 4 2AT OP2 HOP2 sing N N 5 2AT "O5'" "C5'" sing N N 6 2AT "C5'" "C4'" sing N N 7 2AT "C5'" "H5'" sing N N 8 2AT "C5'" "H5''" sing N N 9 2AT "C4'" "O4'" sing N N 10 2AT "C4'" "C3'" sing N N 11 2AT "C4'" "H4'" sing N N 12 2AT "O4'" "C1'" sing N N 13 2AT "C1'" N1 sing N N 14 2AT "C1'" "C2'" sing N N 15 2AT "C1'" "H1'" sing N N 16 2AT N1 C6 sing N N 17 2AT N1 C2 sing N N 18 2AT C6 C5 doub N N 19 2AT C6 H6 sing N N 20 2AT C2 O2 doub N N 21 2AT C2 N3 sing N N 22 2AT N3 C4 sing N N 23 2AT N3 HN3 sing N N 24 2AT C4 O4 doub N N 25 2AT C4 C5 sing N N 26 2AT C5 C5M sing N N 27 2AT C5M H71 sing N N 28 2AT C5M H72 sing N N 29 2AT C5M H73 sing N N 30 2AT "C2'" "O2'" sing N N 31 2AT "C2'" "C3'" sing N N 32 2AT "C2'" "H2'" sing N N 33 2AT "O2'" "CB'" sing N N 34 2AT "CB'" "CC'" sing N N 35 2AT "CB'" "HB'1" sing N N 36 2AT "CB'" "HB'2" sing N N 37 2AT "CC'" "CD'" doub N N 38 2AT "CC'" "HC'" sing N N 39 2AT "CD'" "HD'1" sing N N 40 2AT "CD'" "HD'2" sing N N 41 2AT "C3'" "O3'" sing N N 42 2AT "C3'" "H3'" sing N N 43 2AT "O3'" "HO3'" sing N N 44 2AT OP3 HOP3 sing N N 45 DA OP3 P sing N N 46 DA OP3 HOP3 sing N N 47 DA P OP1 doub N N 48 DA P OP2 sing N N 49 DA P "O5'" sing N N 50 DA OP2 HOP2 sing N N 51 DA "O5'" "C5'" sing N N 52 DA "C5'" "C4'" sing N N 53 DA "C5'" "H5'" sing N N 54 DA "C5'" "H5''" sing N N 55 DA "C4'" "O4'" sing N N 56 DA "C4'" "C3'" sing N N 57 DA "C4'" "H4'" sing N N 58 DA "O4'" "C1'" sing N N 59 DA "C3'" "O3'" sing N N 60 DA "C3'" "C2'" sing N N 61 DA "C3'" "H3'" sing N N 62 DA "O3'" "HO3'" sing N N 63 DA "C2'" "C1'" sing N N 64 DA "C2'" "H2'" sing N N 65 DA "C2'" "H2''" sing N N 66 DA "C1'" N9 sing N N 67 DA "C1'" "H1'" sing N N 68 DA N9 C8 sing Y N 69 DA N9 C4 sing Y N 70 DA C8 N7 doub Y N 71 DA C8 H8 sing N N 72 DA N7 C5 sing Y N 73 DA C5 C6 sing Y N 74 DA C5 C4 doub Y N 75 DA C6 N6 sing N N 76 DA C6 N1 doub Y N 77 DA N6 H61 sing N N 78 DA N6 H62 sing N N 79 DA N1 C2 sing Y N 80 DA C2 N3 doub Y N 81 DA C2 H2 sing N N 82 DA N3 C4 sing Y N 83 DC OP3 P sing N N 84 DC OP3 HOP3 sing N N 85 DC P OP1 doub N N 86 DC P OP2 sing N N 87 DC P "O5'" sing N N 88 DC OP2 HOP2 sing N N 89 DC "O5'" "C5'" sing N N 90 DC "C5'" "C4'" sing N N 91 DC "C5'" "H5'" sing N N 92 DC "C5'" "H5''" sing N N 93 DC "C4'" "O4'" sing N N 94 DC "C4'" "C3'" sing N N 95 DC "C4'" "H4'" sing N N 96 DC "O4'" "C1'" sing N N 97 DC "C3'" "O3'" sing N N 98 DC "C3'" "C2'" sing N N 99 DC "C3'" "H3'" sing N N 100 DC "O3'" "HO3'" sing N N 101 DC "C2'" "C1'" sing N N 102 DC "C2'" "H2'" sing N N 103 DC "C2'" "H2''" sing N N 104 DC "C1'" N1 sing N N 105 DC "C1'" "H1'" sing N N 106 DC N1 C2 sing N N 107 DC N1 C6 sing N N 108 DC C2 O2 doub N N 109 DC C2 N3 sing N N 110 DC N3 C4 doub N N 111 DC C4 N4 sing N N 112 DC C4 C5 sing N N 113 DC N4 H41 sing N N 114 DC N4 H42 sing N N 115 DC C5 C6 doub N N 116 DC C5 H5 sing N N 117 DC C6 H6 sing N N 118 DG OP3 P sing N N 119 DG OP3 HOP3 sing N N 120 DG P OP1 doub N N 121 DG P OP2 sing N N 122 DG P "O5'" sing N N 123 DG OP2 HOP2 sing N N 124 DG "O5'" "C5'" sing N N 125 DG "C5'" "C4'" sing N N 126 DG "C5'" "H5'" sing N N 127 DG "C5'" "H5''" sing N N 128 DG "C4'" "O4'" sing N N 129 DG "C4'" "C3'" sing N N 130 DG "C4'" "H4'" sing N N 131 DG "O4'" "C1'" sing N N 132 DG "C3'" "O3'" sing N N 133 DG "C3'" "C2'" sing N N 134 DG "C3'" "H3'" sing N N 135 DG "O3'" "HO3'" sing N N 136 DG "C2'" "C1'" sing N N 137 DG "C2'" "H2'" sing N N 138 DG "C2'" "H2''" sing N N 139 DG "C1'" N9 sing N N 140 DG "C1'" "H1'" sing N N 141 DG N9 C8 sing Y N 142 DG N9 C4 sing Y N 143 DG C8 N7 doub Y N 144 DG C8 H8 sing N N 145 DG N7 C5 sing Y N 146 DG C5 C6 sing N N 147 DG C5 C4 doub Y N 148 DG C6 O6 doub N N 149 DG C6 N1 sing N N 150 DG N1 C2 sing N N 151 DG N1 H1 sing N N 152 DG C2 N2 sing N N 153 DG C2 N3 doub N N 154 DG N2 H21 sing N N 155 DG N2 H22 sing N N 156 DG N3 C4 sing N N 157 DT OP3 P sing N N 158 DT OP3 HOP3 sing N N 159 DT P OP1 doub N N 160 DT P OP2 sing N N 161 DT P "O5'" sing N N 162 DT OP2 HOP2 sing N N 163 DT "O5'" "C5'" sing N N 164 DT "C5'" "C4'" sing N N 165 DT "C5'" "H5'" sing N N 166 DT "C5'" "H5''" sing N N 167 DT "C4'" "O4'" sing N N 168 DT "C4'" "C3'" sing N N 169 DT "C4'" "H4'" sing N N 170 DT "O4'" "C1'" sing N N 171 DT "C3'" "O3'" sing N N 172 DT "C3'" "C2'" sing N N 173 DT "C3'" "H3'" sing N N 174 DT "O3'" "HO3'" sing N N 175 DT "C2'" "C1'" sing N N 176 DT "C2'" "H2'" sing N N 177 DT "C2'" "H2''" sing N N 178 DT "C1'" N1 sing N N 179 DT "C1'" "H1'" sing N N 180 DT N1 C2 sing N N 181 DT N1 C6 sing N N 182 DT C2 O2 doub N N 183 DT C2 N3 sing N N 184 DT N3 C4 sing N N 185 DT N3 H3 sing N N 186 DT C4 O4 doub N N 187 DT C4 C5 sing N N 188 DT C5 C7 sing N N 189 DT C5 C6 doub N N 190 DT C7 H71 sing N N 191 DT C7 H72 sing N N 192 DT C7 H73 sing N N 193 DT C6 H6 sing N N 194 HOH O H1 sing N N 195 HOH O H2 sing N N 196 # _ndb_struct_conf_na.entry_id 1Y9F _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 DG 1 1_555 B DC 10 1_555 -0.341 -0.142 0.151 -0.625 -7.809 -1.470 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.109 -0.083 0.037 5.588 -14.773 0.584 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.382 -0.185 0.157 -6.688 -16.461 0.616 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.132 -0.098 -0.016 -3.818 -15.681 0.702 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B 2AT 6 1_555 0.172 -0.117 0.071 -3.431 -14.760 -2.223 5 A_DA5:2AT16_B A 5 ? B 16 ? 20 1 1 A 2AT 6 1_555 B DA 5 1_555 0.003 -0.131 0.236 5.471 -12.912 2.712 6 A_2AT6:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.010 -0.177 -0.015 6.676 -11.361 2.458 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.200 -0.194 -0.142 11.870 -14.138 -0.160 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.165 -0.175 -0.116 -7.329 -10.468 1.197 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.254 -0.200 -0.016 -0.827 4.324 -1.840 10 A_DC10:DG11_B A 10 ? B 11 ? 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 DG 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 0.308 -1.498 3.131 2.531 -0.927 38.776 -2.142 -0.166 3.177 -1.395 -3.807 38.866 1 AA_DG1DC2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.269 -2.167 3.430 -0.218 11.199 25.988 -6.823 -0.598 2.313 23.559 0.459 28.261 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.116 -1.512 3.158 -2.141 4.709 36.157 -3.029 1.502 3.003 7.539 3.428 36.513 3 AA_DG3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B 2AT 6 1_555 0.675 -1.492 3.221 3.149 18.778 26.115 -5.562 -0.734 1.833 36.083 -6.052 32.221 4 AA_DT4DA5:2AT16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B 2AT 6 1_555 A 2AT 6 1_555 B DA 5 1_555 0.651 -1.313 3.032 -0.199 6.084 32.312 -3.248 -1.180 2.742 10.812 0.353 32.865 5 AA_DA52AT6:DA152AT16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A 2AT 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.154 -1.422 3.106 1.386 14.501 30.324 -4.498 0.462 2.208 25.925 -2.477 33.568 6 AA_2AT6DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 0.118 -1.699 3.242 -0.163 4.511 30.769 -3.995 -0.250 2.968 8.445 0.305 31.090 7 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.416 -2.004 3.665 0.369 13.321 29.616 -5.923 0.810 2.546 24.555 -0.680 32.414 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.164 -1.582 3.261 0.077 1.150 34.931 -2.806 -0.261 3.209 1.915 -0.128 34.949 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 410D _pdbx_initial_refinement_model.details 'pdb entry 410D' #