data_1Y9S # _entry.id 1Y9S # _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 1Y9S pdb_00001y9s 10.2210/pdb1y9s/pdb NDB AD0040 ? ? RCSB RCSB031295 ? ? WWPDB D_1000031295 ? ? # 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 PDB 1Y9F ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-allyl Thymidine (T*) ; unspecified PDB 1YB9 ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(N,N-dimethylaminooxy)ethyl] Thymidine (T*) ; unspecified PDB 1YBC ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(benzyloxy)ethyl] Thymidine (T*) ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Y9S _pdbx_database_status.recvd_initial_deposition_date 2004-12-16 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _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 1Y9S _cell.length_a 24.831 _cell.length_b 44.983 _cell.length_c 45.409 _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 1Y9S _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*(2GT)P*AP*CP*GP*C)-3')" 3099.053 2 ? ? ? ? 2 water nat water 18.015 119 ? ? ? ? # _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)(2GT)(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 2GT 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 1Y9S _struct_ref.pdbx_db_accession 1Y9S _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 1Y9S A 1 ? 10 ? 1Y9S 1 ? 10 ? 1 10 2 1 1Y9S B 1 ? 10 ? 1Y9S 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 2GT 'RNA linking' n ;2'-O-PROPARGYL THYMIDINE-5'-MONOPHOSPHATE ; ? 'C13 H17 N2 O9 P' 376.256 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 1Y9S _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 39.88 _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 1998-08-24 _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 No _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 1Y9S _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3.0 _reflns.d_resolution_high 1.55 _reflns.d_resolution_low 40.0 _reflns.number_all 7408 _reflns.number_obs 7408 _reflns.percent_possible_obs 94.9 _reflns.pdbx_Rmerge_I_obs 0.062 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 23.9 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.8 _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 1.55 _reflns_shell.d_res_low 1.61 _reflns_shell.percent_possible_all 83.0 _reflns_shell.Rmerge_I_obs 0.265 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.0 _reflns_shell.pdbx_redundancy 3.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 626 _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 1Y9S _refine.ls_d_res_high 1.55 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 7257 _refine.ls_number_reflns_obs 7257 _refine.ls_number_reflns_R_free 761 _refine.ls_percent_reflns_obs 93.0 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1626 _refine.ls_R_factor_R_free 0.2049 _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 22.6 _refine.aniso_B[1][1] 2.712 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][2] -5.760 _refine.aniso_B[2][3] 0.000 _refine.aniso_B[3][3] 3.048 _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 125 _refine_hist.number_atoms_total 537 _refine_hist.d_res_high 1.55 _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 1.29 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.55 _refine_ls_shell.d_res_low 1.59 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.2715 _refine_ls_shell.percent_reflns_obs 51.6 _refine_ls_shell.R_factor_R_free 0.3245 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 35 _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 1Y9S _struct.title ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propargyl Thymidine (T*) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Y9S _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;A-DNA decamer, O2'-modification, 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 2GT 6 P ? ? A DA 5 A 2GT 6 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale2 covale both ? A 2GT 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A 2GT 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B 2GT 6 P ? ? B DA 15 B 2GT 16 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale4 covale both ? B 2GT 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B 2GT 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.593 ? ? 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 2GT 6 N3 ? ? A DA 5 B 2GT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B 2GT 6 O4 ? ? A DA 5 B 2GT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 2GT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A 2GT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 2GT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A 2GT 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 1Y9S _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 1Y9S _atom_sites.fract_transf_matrix[1][1] 0.040272 _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] 0.022231 _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] 0.022022 _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 2GT 6 6 6 2GT PRG 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 2GT 6 16 16 2GT PRG 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 3 104 104 HOH HOH A . C 2 HOH 4 105 105 HOH HOH A . C 2 HOH 5 106 106 HOH HOH A . C 2 HOH 6 107 107 HOH HOH A . C 2 HOH 7 108 108 HOH HOH A . C 2 HOH 8 109 109 HOH HOH A . C 2 HOH 9 110 110 HOH HOH A . C 2 HOH 10 112 112 HOH HOH A . C 2 HOH 11 113 113 HOH HOH A . C 2 HOH 12 114 114 HOH HOH A . C 2 HOH 13 115 115 HOH HOH A . C 2 HOH 14 118 118 HOH HOH A . C 2 HOH 15 119 119 HOH HOH A . C 2 HOH 16 120 120 HOH HOH A . C 2 HOH 17 127 127 HOH HOH A . C 2 HOH 18 128 128 HOH HOH A . C 2 HOH 19 129 129 HOH HOH A . C 2 HOH 20 130 130 HOH HOH A . C 2 HOH 21 132 132 HOH HOH A . C 2 HOH 22 133 133 HOH HOH A . C 2 HOH 23 134 134 HOH HOH A . C 2 HOH 24 136 136 HOH HOH A . C 2 HOH 25 138 138 HOH HOH A . C 2 HOH 26 139 139 HOH HOH A . C 2 HOH 27 142 142 HOH HOH A . C 2 HOH 28 145 145 HOH HOH A . C 2 HOH 29 146 146 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 35 153 153 HOH HOH A . C 2 HOH 36 154 154 HOH HOH A . C 2 HOH 37 156 156 HOH HOH A . C 2 HOH 38 157 157 HOH HOH A . C 2 HOH 39 158 158 HOH HOH A . C 2 HOH 40 159 159 HOH HOH A . C 2 HOH 41 160 160 HOH HOH A . C 2 HOH 42 162 162 HOH HOH A . C 2 HOH 43 163 163 HOH HOH A . C 2 HOH 44 165 165 HOH HOH A . C 2 HOH 45 170 170 HOH HOH A . C 2 HOH 46 171 171 HOH HOH A . C 2 HOH 47 174 174 HOH HOH A . C 2 HOH 48 175 175 HOH HOH A . C 2 HOH 49 176 176 HOH HOH A . C 2 HOH 50 183 183 HOH HOH A . C 2 HOH 51 185 185 HOH HOH A . C 2 HOH 52 187 187 HOH HOH A . C 2 HOH 53 188 188 HOH HOH A . C 2 HOH 54 189 189 HOH HOH A . C 2 HOH 55 190 190 HOH HOH A . C 2 HOH 56 191 191 HOH HOH A . C 2 HOH 57 192 192 HOH HOH A . C 2 HOH 58 193 193 HOH HOH A . C 2 HOH 59 194 194 HOH HOH A . C 2 HOH 60 195 195 HOH HOH A . C 2 HOH 61 196 196 HOH HOH A . C 2 HOH 62 197 197 HOH HOH A . C 2 HOH 63 201 201 HOH HOH A . C 2 HOH 64 202 202 HOH HOH A . C 2 HOH 65 204 204 HOH HOH A . C 2 HOH 66 205 205 HOH HOH A . C 2 HOH 67 206 206 HOH HOH A . C 2 HOH 68 207 207 HOH HOH A . C 2 HOH 69 208 208 HOH HOH A . C 2 HOH 70 210 210 HOH HOH A . C 2 HOH 71 213 213 HOH HOH A . C 2 HOH 72 214 214 HOH HOH A . C 2 HOH 73 215 215 HOH HOH A . C 2 HOH 74 217 217 HOH HOH A . C 2 HOH 75 219 219 HOH HOH A . D 2 HOH 1 103 103 HOH HOH B . D 2 HOH 2 111 111 HOH HOH B . D 2 HOH 3 116 116 HOH HOH B . D 2 HOH 4 117 117 HOH HOH B . D 2 HOH 5 121 121 HOH HOH B . D 2 HOH 6 122 122 HOH HOH B . D 2 HOH 7 123 123 HOH HOH B . D 2 HOH 8 124 124 HOH HOH B . D 2 HOH 9 125 125 HOH HOH B . D 2 HOH 10 126 126 HOH HOH B . D 2 HOH 11 131 131 HOH HOH B . D 2 HOH 12 135 135 HOH HOH B . D 2 HOH 13 137 137 HOH HOH B . D 2 HOH 14 140 140 HOH HOH B . D 2 HOH 15 141 141 HOH HOH B . D 2 HOH 16 143 143 HOH HOH B . D 2 HOH 17 144 144 HOH HOH B . D 2 HOH 18 147 147 HOH HOH B . D 2 HOH 19 155 155 HOH HOH B . D 2 HOH 20 161 161 HOH HOH B . D 2 HOH 21 164 164 HOH HOH B . D 2 HOH 22 166 166 HOH HOH B . D 2 HOH 23 167 167 HOH HOH B . D 2 HOH 24 168 168 HOH HOH B . D 2 HOH 25 169 169 HOH HOH B . D 2 HOH 26 172 172 HOH HOH B . D 2 HOH 27 173 173 HOH HOH B . D 2 HOH 28 177 177 HOH HOH B . D 2 HOH 29 178 178 HOH HOH B . D 2 HOH 30 179 179 HOH HOH B . D 2 HOH 31 180 180 HOH HOH B . D 2 HOH 32 181 181 HOH HOH B . D 2 HOH 33 182 182 HOH HOH B . D 2 HOH 34 184 184 HOH HOH B . D 2 HOH 35 186 186 HOH HOH B . D 2 HOH 36 198 198 HOH HOH B . D 2 HOH 37 199 199 HOH HOH B . D 2 HOH 38 200 200 HOH HOH B . D 2 HOH 39 203 203 HOH HOH B . D 2 HOH 40 209 209 HOH HOH B . D 2 HOH 41 211 211 HOH HOH B . D 2 HOH 42 212 212 HOH HOH B . D 2 HOH 43 216 216 HOH HOH B . D 2 HOH 44 218 218 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 2GT 6 A 2GT 6 ? DT ? 2 B 2GT 6 B 2GT 16 ? DT ? # _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_ _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 2GT P P N N 1 2GT OP1 O N N 2 2GT OP2 O N N 3 2GT "O5'" O N N 4 2GT "C5'" C N N 5 2GT "C4'" C N R 6 2GT "O4'" O N N 7 2GT "C1'" C N R 8 2GT N1 N N N 9 2GT C6 C N N 10 2GT C2 C N N 11 2GT O2 O N N 12 2GT N3 N N N 13 2GT C4 C N N 14 2GT O4 O N N 15 2GT C5 C N N 16 2GT C5M C N N 17 2GT "C2'" C N R 18 2GT "O2'" O N N 19 2GT "CB'" C N N 20 2GT "CC'" C N N 21 2GT "CD'" C N N 22 2GT "C3'" C N R 23 2GT "O3'" O N N 24 2GT OP3 O N N 25 2GT HOP2 H N N 26 2GT "H5'" H N N 27 2GT "H5''" H N N 28 2GT "H4'" H N N 29 2GT "H1'" H N N 30 2GT H6 H N N 31 2GT HN3 H N N 32 2GT H71 H N N 33 2GT H72 H N N 34 2GT H73 H N N 35 2GT "H2'" H N N 36 2GT "HB'1" H N N 37 2GT "HB'2" H N N 38 2GT "HD'" H N N 39 2GT "H3'" H N N 40 2GT "HO3'" H N N 41 2GT HOP3 H N N 42 DA OP3 O N N 43 DA P P N N 44 DA OP1 O N N 45 DA OP2 O N N 46 DA "O5'" O N N 47 DA "C5'" C N N 48 DA "C4'" C N R 49 DA "O4'" O N N 50 DA "C3'" C N S 51 DA "O3'" O N N 52 DA "C2'" C N N 53 DA "C1'" C N R 54 DA N9 N Y N 55 DA C8 C Y N 56 DA N7 N Y N 57 DA C5 C Y N 58 DA C6 C Y N 59 DA N6 N N N 60 DA N1 N Y N 61 DA C2 C Y N 62 DA N3 N Y N 63 DA C4 C Y N 64 DA HOP3 H N N 65 DA HOP2 H N N 66 DA "H5'" H N N 67 DA "H5''" H N N 68 DA "H4'" H N N 69 DA "H3'" H N N 70 DA "HO3'" H N N 71 DA "H2'" H N N 72 DA "H2''" H N N 73 DA "H1'" H N N 74 DA H8 H N N 75 DA H61 H N N 76 DA H62 H N N 77 DA H2 H N N 78 DC OP3 O N N 79 DC P P N N 80 DC OP1 O N N 81 DC OP2 O N N 82 DC "O5'" O N N 83 DC "C5'" C N N 84 DC "C4'" C N R 85 DC "O4'" O N N 86 DC "C3'" C N S 87 DC "O3'" O N N 88 DC "C2'" C N N 89 DC "C1'" C N R 90 DC N1 N N N 91 DC C2 C N N 92 DC O2 O N N 93 DC N3 N N N 94 DC C4 C N N 95 DC N4 N N N 96 DC C5 C N N 97 DC C6 C N N 98 DC HOP3 H N N 99 DC HOP2 H N N 100 DC "H5'" H N N 101 DC "H5''" H N N 102 DC "H4'" H N N 103 DC "H3'" H N N 104 DC "HO3'" H N N 105 DC "H2'" H N N 106 DC "H2''" H N N 107 DC "H1'" H N N 108 DC H41 H N N 109 DC H42 H N N 110 DC H5 H N N 111 DC H6 H N N 112 DG OP3 O N N 113 DG P P N N 114 DG OP1 O N N 115 DG OP2 O N N 116 DG "O5'" O N N 117 DG "C5'" C N N 118 DG "C4'" C N R 119 DG "O4'" O N N 120 DG "C3'" C N S 121 DG "O3'" O N N 122 DG "C2'" C N N 123 DG "C1'" C N R 124 DG N9 N Y N 125 DG C8 C Y N 126 DG N7 N Y N 127 DG C5 C Y N 128 DG C6 C N N 129 DG O6 O N N 130 DG N1 N N N 131 DG C2 C N N 132 DG N2 N N N 133 DG N3 N N N 134 DG C4 C Y N 135 DG HOP3 H N N 136 DG HOP2 H N N 137 DG "H5'" H N N 138 DG "H5''" H N N 139 DG "H4'" H N N 140 DG "H3'" H N N 141 DG "HO3'" H N N 142 DG "H2'" H N N 143 DG "H2''" H N N 144 DG "H1'" H N N 145 DG H8 H N N 146 DG H1 H N N 147 DG H21 H N N 148 DG H22 H N N 149 DT OP3 O N N 150 DT P P N N 151 DT OP1 O N N 152 DT OP2 O N N 153 DT "O5'" O N N 154 DT "C5'" C N N 155 DT "C4'" C N R 156 DT "O4'" O N N 157 DT "C3'" C N S 158 DT "O3'" O N N 159 DT "C2'" C N N 160 DT "C1'" C N R 161 DT N1 N N N 162 DT C2 C N N 163 DT O2 O N N 164 DT N3 N N N 165 DT C4 C N N 166 DT O4 O N N 167 DT C5 C N N 168 DT C7 C N N 169 DT C6 C N N 170 DT HOP3 H N N 171 DT HOP2 H N N 172 DT "H5'" H N N 173 DT "H5''" H N N 174 DT "H4'" H N N 175 DT "H3'" H N N 176 DT "HO3'" H N N 177 DT "H2'" H N N 178 DT "H2''" H N N 179 DT "H1'" H N N 180 DT H3 H N N 181 DT H71 H N N 182 DT H72 H N N 183 DT H73 H N N 184 DT H6 H N N 185 HOH O O N N 186 HOH H1 H N N 187 HOH H2 H N N 188 # 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 2GT P OP1 doub N N 1 2GT P OP2 sing N N 2 2GT P "O5'" sing N N 3 2GT P OP3 sing N N 4 2GT OP2 HOP2 sing N N 5 2GT "O5'" "C5'" sing N N 6 2GT "C5'" "C4'" sing N N 7 2GT "C5'" "H5'" sing N N 8 2GT "C5'" "H5''" sing N N 9 2GT "C4'" "O4'" sing N N 10 2GT "C4'" "C3'" sing N N 11 2GT "C4'" "H4'" sing N N 12 2GT "O4'" "C1'" sing N N 13 2GT "C1'" N1 sing N N 14 2GT "C1'" "C2'" sing N N 15 2GT "C1'" "H1'" sing N N 16 2GT N1 C6 sing N N 17 2GT N1 C2 sing N N 18 2GT C6 C5 doub N N 19 2GT C6 H6 sing N N 20 2GT C2 O2 doub N N 21 2GT C2 N3 sing N N 22 2GT N3 C4 sing N N 23 2GT N3 HN3 sing N N 24 2GT C4 O4 doub N N 25 2GT C4 C5 sing N N 26 2GT C5 C5M sing N N 27 2GT C5M H71 sing N N 28 2GT C5M H72 sing N N 29 2GT C5M H73 sing N N 30 2GT "C2'" "O2'" sing N N 31 2GT "C2'" "C3'" sing N N 32 2GT "C2'" "H2'" sing N N 33 2GT "O2'" "CB'" sing N N 34 2GT "CB'" "CC'" sing N N 35 2GT "CB'" "HB'1" sing N N 36 2GT "CB'" "HB'2" sing N N 37 2GT "CC'" "CD'" trip N N 38 2GT "CD'" "HD'" sing N N 39 2GT "C3'" "O3'" sing N N 40 2GT "C3'" "H3'" sing N N 41 2GT "O3'" "HO3'" sing N N 42 2GT OP3 HOP3 sing N N 43 DA OP3 P sing N N 44 DA OP3 HOP3 sing N N 45 DA P OP1 doub N N 46 DA P OP2 sing N N 47 DA P "O5'" sing N N 48 DA OP2 HOP2 sing N N 49 DA "O5'" "C5'" sing N N 50 DA "C5'" "C4'" sing N N 51 DA "C5'" "H5'" sing N N 52 DA "C5'" "H5''" sing N N 53 DA "C4'" "O4'" sing N N 54 DA "C4'" "C3'" sing N N 55 DA "C4'" "H4'" sing N N 56 DA "O4'" "C1'" sing N N 57 DA "C3'" "O3'" sing N N 58 DA "C3'" "C2'" sing N N 59 DA "C3'" "H3'" sing N N 60 DA "O3'" "HO3'" sing N N 61 DA "C2'" "C1'" sing N N 62 DA "C2'" "H2'" sing N N 63 DA "C2'" "H2''" sing N N 64 DA "C1'" N9 sing N N 65 DA "C1'" "H1'" sing N N 66 DA N9 C8 sing Y N 67 DA N9 C4 sing Y N 68 DA C8 N7 doub Y N 69 DA C8 H8 sing N N 70 DA N7 C5 sing Y N 71 DA C5 C6 sing Y N 72 DA C5 C4 doub Y N 73 DA C6 N6 sing N N 74 DA C6 N1 doub Y N 75 DA N6 H61 sing N N 76 DA N6 H62 sing N N 77 DA N1 C2 sing Y N 78 DA C2 N3 doub Y N 79 DA C2 H2 sing N N 80 DA N3 C4 sing Y N 81 DC OP3 P sing N N 82 DC OP3 HOP3 sing N N 83 DC P OP1 doub N N 84 DC P OP2 sing N N 85 DC P "O5'" sing N N 86 DC OP2 HOP2 sing N N 87 DC "O5'" "C5'" sing N N 88 DC "C5'" "C4'" sing N N 89 DC "C5'" "H5'" sing N N 90 DC "C5'" "H5''" sing N N 91 DC "C4'" "O4'" sing N N 92 DC "C4'" "C3'" sing N N 93 DC "C4'" "H4'" sing N N 94 DC "O4'" "C1'" sing N N 95 DC "C3'" "O3'" sing N N 96 DC "C3'" "C2'" sing N N 97 DC "C3'" "H3'" sing N N 98 DC "O3'" "HO3'" sing N N 99 DC "C2'" "C1'" sing N N 100 DC "C2'" "H2'" sing N N 101 DC "C2'" "H2''" sing N N 102 DC "C1'" N1 sing N N 103 DC "C1'" "H1'" sing N N 104 DC N1 C2 sing N N 105 DC N1 C6 sing N N 106 DC C2 O2 doub N N 107 DC C2 N3 sing N N 108 DC N3 C4 doub N N 109 DC C4 N4 sing N N 110 DC C4 C5 sing N N 111 DC N4 H41 sing N N 112 DC N4 H42 sing N N 113 DC C5 C6 doub N N 114 DC C5 H5 sing N N 115 DC C6 H6 sing N N 116 DG OP3 P sing N N 117 DG OP3 HOP3 sing N N 118 DG P OP1 doub N N 119 DG P OP2 sing N N 120 DG P "O5'" sing N N 121 DG OP2 HOP2 sing N N 122 DG "O5'" "C5'" sing N N 123 DG "C5'" "C4'" sing N N 124 DG "C5'" "H5'" sing N N 125 DG "C5'" "H5''" sing N N 126 DG "C4'" "O4'" sing N N 127 DG "C4'" "C3'" sing N N 128 DG "C4'" "H4'" sing N N 129 DG "O4'" "C1'" sing N N 130 DG "C3'" "O3'" sing N N 131 DG "C3'" "C2'" sing N N 132 DG "C3'" "H3'" sing N N 133 DG "O3'" "HO3'" sing N N 134 DG "C2'" "C1'" sing N N 135 DG "C2'" "H2'" sing N N 136 DG "C2'" "H2''" sing N N 137 DG "C1'" N9 sing N N 138 DG "C1'" "H1'" sing N N 139 DG N9 C8 sing Y N 140 DG N9 C4 sing Y N 141 DG C8 N7 doub Y N 142 DG C8 H8 sing N N 143 DG N7 C5 sing Y N 144 DG C5 C6 sing N N 145 DG C5 C4 doub Y N 146 DG C6 O6 doub N N 147 DG C6 N1 sing N N 148 DG N1 C2 sing N N 149 DG N1 H1 sing N N 150 DG C2 N2 sing N N 151 DG C2 N3 doub N N 152 DG N2 H21 sing N N 153 DG N2 H22 sing N N 154 DG N3 C4 sing N N 155 DT OP3 P sing N N 156 DT OP3 HOP3 sing N N 157 DT P OP1 doub N N 158 DT P OP2 sing N N 159 DT P "O5'" sing N N 160 DT OP2 HOP2 sing N N 161 DT "O5'" "C5'" sing N N 162 DT "C5'" "C4'" sing N N 163 DT "C5'" "H5'" sing N N 164 DT "C5'" "H5''" sing N N 165 DT "C4'" "O4'" sing N N 166 DT "C4'" "C3'" sing N N 167 DT "C4'" "H4'" sing N N 168 DT "O4'" "C1'" sing N N 169 DT "C3'" "O3'" sing N N 170 DT "C3'" "C2'" sing N N 171 DT "C3'" "H3'" sing N N 172 DT "O3'" "HO3'" sing N N 173 DT "C2'" "C1'" sing N N 174 DT "C2'" "H2'" sing N N 175 DT "C2'" "H2''" sing N N 176 DT "C1'" N1 sing N N 177 DT "C1'" "H1'" sing N N 178 DT N1 C2 sing N N 179 DT N1 C6 sing N N 180 DT C2 O2 doub N N 181 DT C2 N3 sing N N 182 DT N3 C4 sing N N 183 DT N3 H3 sing N N 184 DT C4 O4 doub N N 185 DT C4 C5 sing N N 186 DT C5 C7 sing N N 187 DT C5 C6 doub N N 188 DT C7 H71 sing N N 189 DT C7 H72 sing N N 190 DT C7 H73 sing N N 191 DT C6 H6 sing N N 192 HOH O H1 sing N N 193 HOH O H2 sing N N 194 # _ndb_struct_conf_na.entry_id 1Y9S _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 -0.282 -0.120 0.136 3.166 -5.772 -0.176 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.116 -0.008 0.007 6.623 -15.124 0.711 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.337 -0.140 -0.111 -9.527 -16.031 1.694 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.177 -0.094 0.072 -4.355 -14.841 0.672 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B 2GT 6 1_555 0.232 -0.065 0.119 -2.808 -14.842 -4.649 5 A_DA5:2GT16_B A 5 ? B 16 ? 20 1 1 A 2GT 6 1_555 B DA 5 1_555 -0.143 -0.130 0.259 6.003 -12.455 4.204 6 A_2GT6:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.039 -0.147 0.003 6.435 -10.541 2.380 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.223 -0.157 -0.181 10.292 -13.833 1.103 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.210 -0.140 -0.102 -6.998 -11.297 1.121 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.161 -0.193 0.125 -2.478 5.582 -1.450 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 0.237 -1.415 3.206 2.205 -0.527 39.181 -2.045 -0.094 3.233 -0.785 -3.285 39.244 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 0.304 -2.122 3.621 1.976 10.943 25.008 -7.155 -0.162 2.504 23.825 -4.302 27.333 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 -1.101 -1.441 3.088 -4.183 4.847 35.722 -2.949 1.221 2.979 7.823 6.753 36.273 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 2GT 6 1_555 0.587 -1.587 3.157 2.466 19.686 26.894 -5.472 -0.685 1.684 36.658 -4.591 33.312 4 AA_DT4DA5:2GT16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B 2GT 6 1_555 A 2GT 6 1_555 B DA 5 1_555 0.772 -1.384 3.018 0.011 5.759 31.500 -3.430 -1.399 2.729 10.498 -0.021 32.009 5 AA_DA52GT6:DA152GT16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A 2GT 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.266 -1.395 3.082 1.259 13.036 31.361 -4.192 0.630 2.323 22.905 -2.212 33.922 6 AA_2GT6DA7: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 0.217 -1.696 3.283 1.479 4.168 30.872 -3.926 -0.129 3.040 7.780 -2.761 31.179 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 -0.364 -1.940 3.601 -0.239 13.360 28.936 -5.928 0.622 2.488 25.116 0.449 31.812 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 0.149 -1.683 3.280 -0.480 1.564 34.958 -3.032 -0.320 3.201 2.602 0.799 34.995 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' #